Jo Anne B. Ross, the associate commissioner of Social Security for family assistance for the past three years, resigned abruptly Thursday night, sources said yesterday.

Ross reportedly quit a few minutes after learning that Wayne Stanton, regional director of the Department of Health and Human Services for the midwestern region, was being appointed by HHS Secretary Otis R. Bowen to head HHS' new Family Support Administration. Stanton was an aide to Bowen when the secretary was governor of Indiana.

Ross, also a candidate for the job, could not be reached for comment.

The FSA will include the Aid to Families with Dependent Children program, which Ross has headed for three years. Under the AFDC program, about 10.8 million poor mothers (and a small number of fathers) and children get monthly welfare support payments from the states. The federal government reimburses the states for one-half to four-fifths of the costs, with poorer states receiving the higher reimbursement ratios. The federal outlay for the program in fiscal 1986 is about $9 billion.

The AFDC program is by far the biggest unit of the new FSA. FSA includes refugee assistance, the low-income energy assistance program, the Child-Support Enforcement program, the Community Services block grant and the Work Incentive programs.

Bowen combined administration of these programs into a single unit to give increased emphasis to the goal of strengthening the family. Total outlays by FSA, with an estimated 1,025 employes, are expected to be $11.5 billion in fiscal 1987.

In a memorandum circulated among AFDC employes yesterday, Ross said her resignation was the result of "the decision to appoint Wayne Stanton."

Thomas R. Burke, department chief of staff, said Bowen was "very high on her" and had proposed to make Ross deputy FSA administrator. The sources said Ross did not want to be Stanton's subordinate.