Both of his parents were physicians; his mother Helene Deutsch was a professor of psychiatry at the University of Vienna and a student and colleague of Sigmund Freud.

In 1939, he married Suzanne Zeitlin, a native Bostonian who had just graduated from Simmons College with a master's degree in social work.

Martin earned his Ph.D. in physics in 1941, under Robley D. Evans leading to a thesis entitled: A Study of Nuclear Radiations by Means of a Magnetic Lens Beta Ray Spectrometer.

Deutsch arrived at Los Alamos in 1943, and began working closely with Emilio Segrè on problems concerning fission physics.

Deutsch returned to MIT in 1946, joining his Los Alamos colleagues Victor Weisskopf and Bruno Rossi.