Robert H. McKinney, chairman of the Federal Home Loan Bank Board, said yesterday he will resign from the post for "strictly personal" reasons.

He said he plans to return to Indianapolis where he has numerous business and political interests. The main reason for his resignation, he said, is to "have more free time" to spend with his family.

McKinney, 53, submitted his resignation to President Carter April 20, and the president accepted in a May 1 letter "with deep regret." McKinney said he was uncertain of exactly when he could leave the board.

A classmate of Carter's at the U.S. Naval Academy ('46), McKinney chaired the president's 1976 campaign in Indiana. He said he and Carter had discussed "a role" for him in a re-election campaign, but he added: "That's all I'm free to say."

At a press conference yesterday in his office at the bank board, McKinney said he has "no such plan" to run for governor of Indiana.

It has been rumoured that McKinney would seek the office-now held by popular, two-term Republican Otis R. Bowen-which becomes vacant in 1981.

McKinney, who went through rugged confirmation hearings nearly two years ago when he was nominated, has been applauded widely for his performance as chairman.

During the hearings, there allegations of conflicts of interest by congressional critics because of his overlapping business and professional interests in Indianapolis.

McKinney was senior partner in the law firm that was counsel to First Federal Savings & Loan association in Indianapolis, where he was chairman. He was also chairman of a building supplies company that has a life insurance subsidiary.

Civil rights and consumer groups also opposed him because they claimed his S&L had shunned lending to the inner city.

But yesterday, some of his former critics on the Hill described his resignation as a "loss." And Mckinney himself issued a press release listing his "major accomplishments," most of which were not anticipated during his confirmation hearings.

The FHLBB oversees most of the nation's $400 billion savings and loan industry, insures deposits up to $40,000 in most S&Ls, and also serves as a lender to thrift institutions that are strapped for funds.

McKinney has been instrumental in the introduction of money market certificates, on whcih high interest rates have helped attract money to federal S&Ls during periods when they otherwise would have suffered an outflow of funds.

A top board official noted yesterday this is precisely the kind of high interest rate period when S&Ls suffer what is known as disintermediation-an outflow of funds.

But money market certificates have brought deposits of $70 billion to S&Ls, he said. This, in turn, has made more money available for the troubled mortgage market.

McKinney also has pushed various financing alternatives.

Under McKinney, California federal S&Ls were allowed to compete with state thrifts by offering controversial variable rate mortgages, whose rates rise and fall according to a money market index.

S&Ls nationwide also were permitted to offer graduated payment mortgages, which allow for low payments in the beginning of a mortgage, and reverse annuity mortgages, which provide for a retirement income.

President Carter, in his letter, praised McKinney for introducing regulations to help eliminate "red lining"-or discriminatory lending-by thrift institutions.

The FHLBB, under McKinney, created the Community Investment Fund alloting funds to S&Ls at lower than normal rates for mortgages in low-income areas.

McKinney said he told Carter"how highly I regard" Anita Miller, the only other current member of the three-member FHLBB. Miller is considered a possible successor to McKinney.

The third board member, Garth Martson, a Republican, resigned some time ago, and the administration has not come up with a replacement.

McKinney apparently must remain on the board until at least one more person is nominated and confirmed. The board cannot function without a quorum of two, according to a FHLBB official. CAPTION: Picture, FHLBB Chairman Robert H. McKinneey announcing yesterday he will resign. By Ken Feil-The Washington Post