The big losers in Tuesday's Senate voting were liberals, whose rank and morale were both depleted.

Republicans gained three seats raising their total to 41. But the new Senate will more conservative than that numbers suggests. Some committees will have to be realigned, giving Republicans more votes than they had in the 95th Congress that just ended.

Several aides to liberal senators express deep dismay yesterday at the defeats of Sen. Thomas J. McIntyre (D-N.H.), Dick Clark (D-Iowa), Floyd Haskett (D-Colo.), Wendell R. Anderson (D-Minn.) and William D. Hathaway (D-Maine).

Conservatives were jubilant at the victories of Roger Jepsen in Iowa (who beat Clark), Gordon Humphrey in New Hampshire (MeIntyre) and Rep. William Armstrong in Colorado (Haskell). All three qualify as right-wing Republicans.

Just how these changes will affect substance issues before the Senate is not clear, but in at least one important area, they may be significant.By administration reckoning, the election resulted in a probable net loss of two votes for a strategic arms limitation treaty (SALT) with the Soviet Union, even though SALT was not an explicit issue in the campaign this year.

The potential damage to SALT's chances may have been greater than that, however, because of the defeat of McIntyre, a key moderate on the Armed Services Committee who was expected to influence other middle-of-the-road senators in favor of SALT.

McIntyre's departure from Armed Services will have a marked effect on the complexion of that committee, several expert observers agreed yesterday.

Another committee that will be changed substantially by the voting is Finance, where the two most liberal members - Hathaway and Haskell - were both defeated, and the ranking Republican, Carl Curtis of Nebraska, retired.

Finance is one of the committees that will probably have to add a new Republican member next year. The Senate majority and minority leaders will decide on the new distribution of committee seats before Congress reconvenes in January. Republicans will be entitled to 41 percent of all committee seats.

The blows to liberal morale may have been more serious than actual liberal losses. Tuesday's voting gave liberal Democrats almost nothing to cheer about, and sent shivers of anxiety up numerous senatorial spines - those belonging to liberal Democrats who will be running in 1980.

The only shiny linings that liberals saw in the conservative cloud - and they looked to some more like tinsel than silver - were in Michigan and Alabama. Carl Levin, former president of the Detroit City Council and a mainstream liberal Democrat, defeated incumbent Sen. Robert P. Griffin (R-Mich.), and in Alabama a young progressive, Donald Stewart, 38, won the seat held by the late arch-conservative James B. Allen and, after his death, his widow, Maryon Allen.

The other new liberals in the Senate will be Paul E. Tsongas, 37, from Massachusetts, and Bill Bradley, 35, of New Jersey, but they replace liberal Republicans Edward W. Brooke and Clifford P. Case.

The Republicans will have a large number of new faces, ranging form moderates like David Durenberger and Rudy Boschwitz of Minnesota to moderates like Nancy Landon Kassehaum from Kansas and William Cohen of Maine, to conservatives like Armstrong, Humphrey and Jepsen. Another conservative Republican, John Warner, is the apparent winner in Virginia.

An aide to Sen. Howard H. Baker Jr. (R-Tenn.) the minority leader, who handily won reelection Tuesday, said Baker was in high spirits yesterday. He spent much of the day talking with 11 newly elected Republicans.

Republican strategists had calculated that the Tuesday voting could give them anywhere from three fewer to give more senators next year. Gaining three seats was "damn good," one of them said.

Democrats had hoped to knock off at least two Republican nemeses, John G. Tower of Texas and Strom Thurmond of South Carolina, but both of them won reelection. Brooks and Griffin - neither particularly noxious to Senate Democrate - were the only incumbent Republicans defeated Tuesday.

Democrats were elected to replaces three retiring Republicans. Probably the biggest ideological reversal in this category was the election of Democratic Gov. J. J. Exon in Nebrarka to replace retiring Carl Curtis, one of the Senate's most conservative Republicans.

With 20 new members, the next Senate will be a changed institution. Next year, there will be clear majority of senators - 56 - who have been elected in the last four elections, beginning in 1972.

The electorate is also turning increasingly to amateur politicans as new senators. Eight of the 20 new faces elected Tuesday never held elected office before, while only nine of them come from the traditional background of governorships or membership in the House.

The number of independently wealthy senators also increased as a result of Tuesday's voting.

The precise effect of the election on the Senate's committees won't be known until the new Congress organizes itself in January, but some of the changes can be foreseen.

The Senate-Foreign Relations Committee will be transformed, getting a new chairman (Frank Church of Idaho), and several new members. One committee staff member noted yesterday that the defeat of Clark leaves a 32-year-old, Joseph Biden of Delaware, the fourth-ranking Democrat on the committee, separated from the chairmanship by three much older senators. "We may be looking forward to a long Biden chairmanship at the end of this century," this source speculated.

The powerful Appropriations Committee will get only a handful of new members, none at all on the Democratic side. Finance will have a large turnover.

Senate sources predicted no changes in the elected Democratic and Republican leadership, though some consider a challenge to Sen. Ted Stevens (R-Alaska), the Republican whip, possible.

The increased conservative strength in the Senate diminishes the prospects for liberalizing Senate rule changes, which Majority Leader Robert C. Byrd (D-W.Va.) has said he will propose in January.

Byrd is particularly concerned about Senate filibusters that permit a minority to stymie the work of the entire body. But these elections have increased the size of the Senate minority, thus increasing the number of members who could feel a direct interest in maintaining the status quo.

Some of the new senators elected Tuesday are ideological question marks. Gov. David Boren of Oklahoma, for example, has a reputation as a conservative Democrat, but he was also and early supporter of Jimmy Carter's presidential campaign, and the administration hopes to win his votes on at least some issues. Boren replaces retiring conservative Republican Dewey F. Bartlett.

Gov. David Pryor of Arkansas, another newly elected senator, was regarded as a liberal when he served here in the House, but he has moved to the right since, and it is unclear where he may land as a senator.