Upon publication, The Making of the Atomic Bomb enjoyed both critical acclaim and popular success. Rhodes was rewarded for his years of meticulous research when he won the 1987 National Book Award, the 1988 Pulitzer Prize for General Nonfiction, and the 1988 National Book Critics Circle Award for General Nonfiction.

Critics praise Rhodes for his exhaustive research, comprehensive scope, even-handed reportage, and narrative skills in rendering a nearly overwhelming array of historical information into a dramatic story, successfully integrating clear explanation of complex scientific concepts with a humanizing account of the scientists, military officials, and political figures involved in the Manhattan Project.

Solly Zuckerman, in a 1988 review in the New Republic, calls it "a monumental study," and, echoing the widespread praise Rhodes received, asserts:

Rhodes' book richly deserves the acclaim that it has already been accorded. He has taken infinite trouble to understand and to outline in simple language...