President Reagan has chosen Brent Scowcroft, former national security affairs adviser to President Ford and a close associate of former secretary of state Henry A. Kissinger, to head a new advisory commission to recommend a deployment system for the MX missile.

A senior administration official said Scowcroft was recommended by national security affairs adviser William P. Clark. Scowcroft, who was deputy White House national security adviser under Kissinger during the final two years of the Nixon administration, became national security adviser under Ford, and now is a partner in the consulting firm of Kissinger Associates Inc.

Administration sources also confirmed that Carter administration defense secretary Harold Brown will be named to the MX deployment commission. But they said that Ford administration defense secretary James R. Schlesinger would not be on it, as previous reports had forecast.

With conflict-of-interest checks still proceeding on others being considered for the advisory body, announcement of its membership is not expected before Friday or early next week.

The commission of seven to 10 members will be instucted to submit a report to the president within 60 days on how and where it recommends that the MX missile should be based. Congress has held up production money for the intercontinental nuclear weapon until the administration comes up with an acceptable basing plan.

The "Dense Pack" closely spaced formation of 100 missiles near Warren Air Force Base in Wyoming, which stirred considerable opposition after being proposed by Reagan, remains one of several alternatives to be considered by the new commission.

Scowcroft served on an earlier panel, chaired by Nobel prize-winning physicist Charles Townes, which recommended putting the MX in airplanes, and as a possible interim solution putting it into the silos of the Minuteman missiles it is supposed to replace. Both plans were rejected.

He is a member of the Mormon Church, which strongly opposed President Carter's plan for scattering 200 MX missiles in 1,000 or more new silos dispersed across the Nevada and Utah desert.

The Reagan administration has argued that speedy development of the MX is needed as a bargaining chip in strategic arms reduction talks (START) with the Soviet Union. Referring to those negotiations today, administration officials sounded somewhat more optimistic about the possibility of achieving a new U.S.-Soviet strategic nuclear arms control agreement in 1983.

The U.S. negotiator at the START talks in Geneva, Edward L. Rowny, said on NBC that genuine progress had been made in the past six months and there was a "50-50" chance of reaching an agreement with the Soviets in the talks that will resume early next year.

Other administration officials quickly warned reporters that they should not become overly optimistic about the prospects for such a pact, however. White House spokesman Larry Speakes emphasized that any arms control agreement depended on "good Soviet intentions." Another official said, more bluntly: "Rowny is hopeful as are we all. But he wasn't making a forecast. We have no new signal from the Soviets."

But the president seemed as hopeful as his arms control negotiator. On arrival in Palm Springs after a short flight from Los Angeles, Reagan, asked about Rowny's comment, replied:

''I haven't heard that [the ''50-50'' comment], but I know by talking with them, they [the negotiators] feel the soviets really are negotiating in good earnest, so we're a little optimistic.''

Reagan arrived in Palm Springs on Air Force One for a round of holdiay parties after conferring with Clark and deputy chief of staff Michael K. Deaver.

The president is scheduled to meet again with Clark and Secretary of State George P. Shultz in Palm Springs on Friday. Speakes said that Shultz would be in Palm Springs primarily to attend a black-tie New Year's Eve party at the estate of Walter and Lenore Annenberg, where the Reagans will spend the rest of the week.

The Reagans will be in virtual seclusion during this time. One administration official, referring to the lagging economy and high unemployment rate, said that "now is not the time" for the Reagans to be seen conspicuously in black tie and fancy dress.

But the Reagans' schedule this year is little different from what it has been in the past. As private citizen, governor and president, Reagan has always valued his privacy, and he is not representing his trip here as a working vacation.

Nor, despite a spate of published reports about prospective changes in economic policies, is there any indication that Reagan has lost faith in his economic program.

"I don't think that the president's faith in his program has diminished one iota," Speakes said.

Despite negative forecasts from some of his economic advisers, Reagan was described by Speakes as believing that the economy was on the right course and would show significant recovery this year. Reagan expressed a similar view earlier this month in an interview with The Washington Post.