Haywood was transferred to the headquarters of the Manhattan Project on 12 April 1946. He was one of a number West Point graduates from the top ten percent of their classes who were transferred to the Manhattan Project at this time by the Secretary of War, Robert P. Patterson, at the request of the Manhattan Project's commander, Major General Leslie R. Groves, Jr., and over the objection of senior Army leaders. Their job was to replace reservists who had worked for the Project during the war and now were eligible for separation from the Army. Haywood participated in Operation Crossroads, observing the nuclear tests at Bikini Atoll. Groves hoped that a new, permanent agency would soon be created to take over the responsibilities of the wartime Manhattan Project, but passage of the Atomic Energy Act of 1946 through Congress took much longer than expected, and involved considerable debate about the proper role of the military with respect to the development, production and control of nuclear weapons. The act that was finally signed by President Harry S. Truman on 1 August 1946 created a civilian agency, the Atomic Energy Commission, to take over the functions and assets of the Manhattan Project, but the AEC did not assume its role until 1 January 1947. At this point, Haywood was seconded to the AEC's Directorate of Research. Although he had been a colonel in the Army of the United States, Haywood only held the substantive rank of captain in the Army Corps of Engineers. His Army of the United States rank was terminated on 30 June 1947, and he returned to duty with the War Department General Staff as a captain on 1 July 1947. Haywood elected to transfer to the newly created United States Air Force on 10 December 1947. He became a lieutenant colonel on 1 July 1948, and was assigned to the Air Plans Division on 29 August 1948,. where he was involved in drawing up nuclear war plans. From July 1949 to May 1950 he attended the Air War College at Maxwell Air Force Base, Alabama. Haywood was seconded to the Los Alamos National Laboratory in New Mexico from February 1950 to October 1951, at a time when the first thermonuclear weapons were being developed. Edward Teller once remarked that "Colonel Haywood is the only military man I would work for." Haywood then served at the chief of the Air Force Office of Scientific Research, and was vice commander of the Atlantic Missile Range until his retirement from active duty in 1953. He remained with the Air Force Reserve, retiring with the rank of brigadier general in 1967.
Later life
After leaving the Air Force, Haywood became the President and chief executive officer, and later the chairman of the board of Huyck Corporation in Stamford, Connecticut. He was also chairman and acting president of the Hudson Institute in Indianapolis. Haywood died in Vero Beach, Florida, on 25 May 2002. He was survived by his daughters, Barbara and Betty, and sons, Richard and Robert. His wife, Helen, had predeceased him.