William Henry Scott, 66, a retired transportation auditor with the General Accounting Office who was active in Masonry, died Sunday at his home in Alexandria. He had arteriosclerosis.

Mr. Scott was born in Providence, R.I. After serving in the Army in Europe during World War II, he returned to Providence and earned a degree in industrial management at Northeastern University. He began his career in transportation with the New Haven Railroad, working his way up from freight and passenger station agent to traveling auditor.

In 1960, he moved to the Washington area and joined the Interstate Commerce Commission. He later transferred to the GAO as a transportation auditor. He retired in 1977 for reasons of health.

Mr. Scott was a 32nd degree Mason. He was a member of Overseas Lodge No. 40 in Cranston, R.I., and of the Albert Pike Consistory in Washington. He also was a past master of National Lodge No. 12 here and was past president of the 1976 Association of Worshipful Masters of the District of Columbia.

Survivors include his wife, Evelyn, of Alexandria, where the family lives; two daughters, Margaret Harris, of Occoquan, and Dorothy Connery, of Falls Church; one sister, Elizabeth Lawson, of Warwick, R.I., and one granddaughter.