President Reagan has decided to nominate former Indiana governor Otis R. Bowen to be secretary of health and human services, replacing Margaret M. Heckler, White House officials said yesterday.

Reagan made the choice yesterday from a list that included Interior Undersecretary Ann Dore McLaughlin. An announcement is expected today, officials said. White House spokesman Peter Roussel had no comment last night on reports of Bowen's selection.

Bowen, 67, a popular two-term governor, would take over one of the government's largest departments, with a budget of $348 billion and about 130,000 employes.

Heckler was nominated by the president to be ambassador to Ireland after White House chief of staff Donald T. Regan expressed dissatisfaction with the way she was administering HHS. Regan has been a key figure in Cabinet appointments since moving to the White House from the Treasury Department earlier this year.

Bowen, a small-town doctor, was elected governor in 1972 after being speaker of the state House of Representatives. He often referred to himself as "Gov. Otis R. Bowen, MD." Property tax cuts were a major issue in his two successful campaigns for four-year terms. He was barred by law from seeking a third term.

Bowen, currently clinical professor of family medicine at the Indiana University School of Medicine, will face difficult budget decisions at HHS in the next year if confirmed by the Senate.

Reagan has decided to seek another round of deep cuts in domestic spending, and many HHS programs are likely to be targeted by the White House in the effort to reduce the federal deficit. Congress has been reluctant to cut these programs.