The Senate yesterday handed President Reagan two decisive victories on his strategic weapons program, approving funds for the B1 bomber and turning back a proposal to cut off research money for basing the MX missile.

The action came on a day the president sent the Senate a strong written warning that any changes in his strategic program would signal a weakening of American resolve and would undermine the country's bargaining position in arms limitations talks.

In a letter to Sen. Ted Stevens (R-Alaska), chairman of the defense appropriations subcommittee, Reagan also said that "a congressional rejection of any major element of our interrelated program would lead to a substantially greater and potentially more dangerous inferiority than would have resulted from the Carter program."

The letter was read into the record shortly before pro-administration forces beat back, 60 to 35, an amendment by Sen. David H. Pryor (D-Ark.) to cut off research funds for the MX.

About 6 1/2 hours of debate later, the Senate rebuffed by an even wider margin, 66 to 28, an amendment by Sen. Ernest F. Hollings (D-S.C.) that would have removed $2.4 billion in fiscal 1982 funds for the B1 bomber and reallocated the bulk of the money to conventional forces and basic readiness programs.

Both of the votes came on amendments to a record $208.5 billion military spending bill that the Senate has been debating for the past four days. The House has passed its version of the bill, and it includes funds for both the B1 and the MX. The Senate is expected to take final action today.

Most of the passion and rhetoric on the floor of the Senate yesterday was focused on the B1, a four-engine, swept-wing manned bomber designed to penetrate enemy air defenses at low altitudes and drop conventional or nuclear bombs, or to stand off at a distance and launch cruise missiles. The long-term strategic weapons plan Reagan announced Oct. 2 calls for building 100 B1s by 1986.

Opposition to the bomber has centered on questions of both cost and capability. The Air Force estimates the 100 planes will cost $28 billion (with inflation), while the Congressional Budget Office has estimated it will take $39.8 billion. Either figure would make it the most expensive bomber in history.

Hollings called the plane a "$400 million monstrosity" and cited testimony last month by Defense Secretary Caspar W. Weinberger that the plane would be unable to penetrate Soviet air defenses after 1990. Weinberger told the Senate Armed Services Committee Nov. 5 that flights into Soviet territory after that date would be "suicide missions."

That testimony gave considerable ammunition to B1 opponents, and Weinberger has since retracted it. He now says the B1 will serve as a penetrating bomber well into the 1990s, when the Stealth or Advanced Technology Bomber will be ready to replace it as the nation's principal penetrating war plane.

In defense of the B1, Stevens, who had expressed early skepticism, argued that the country has to "have a bridge between the Edsel" and the Stealth. His "Edsel" reference was to the Air Force's aging fleet of B52s, which the B1s are designed to replace.

Opponents of the B1 argued that the nation could not afford to develop two new bombers simultaneously without making unacceptable cuts in readiness and conventional forces. Hollings' amendment would restore funds for such nuts and bolts items as ammunition, spare parts, troop levels, and Navy steaming hours.

The B1 opponents also expressed the fear that the two-bomber approach would eventually force the administration to drain money from the development of the Stealth, a plane whose technology remains to be perfected. However, Sen. John Glenn (D-Ohio), called the Stealth "a paper aircraft on a rubber schedule," and argued that the very uncertainty of its development was a strong inducement to go ahead with the B1.

Pryor's unsuccessful MX amendment would have cut $354 million in fiscal year 1982 for research on a basing mode for the missile.

The night before, the lawmakers overwhelmingly approved a far less restrictive amendment--one that forced the administration to spend the great bulk of the MX research funds on a longterm basing plan rather than on an interim plan to place the missiles in existing, superhardened Titan and Minuteman silos.

Yesterday Senate Republicans who joined in that 90-to-4 vote sought to minimize their differences with President Reagan, who proposed the interim basing plan in October.

Senate Majority Leader Howard H. Baker Jr. (R-Tenn.) argued that the amendment fully endorsed the president's proposal, noting that some $20 million in the 1982 budget approved by the Senate remained available for research on superhardened silos. However, Democratic senators said the clear message of the Tuesday vote was to force the president to move more quickly to a decision on long-term basing.

"It was not repudiation of the president but a strong signal of disapproval," said Pryor.

The Arkansas Democrat also said the purpose of his amendment had been to delay all research on the MX until next spring so that "a consensus" could develop on a basing mode.