The Rape of Nanking is structured into three main parts. The first uses a technique that Chang called "the Rashomon perspective" to narrate the events of the Nanking Massacre, from three different perspectives: that of the Japanese military, the Chinese victims, and the Westerners who tried to help Chinese civilians. The second part concerns the postwar reaction to the massacre, especially that of the American and European governments. The third part of the book examines the circumstances that, Chang believed, have kept knowledge of the massacre out of public consciousness decades after the war.
The book depicted in detail the killing, torture, and rape that occurred during the Nanking Massacre. Chang listed and described the kinds of torture that were visited upon the residents, including live burials, mutilation, "death by fire", "death by ice", and "death by dogs". Based on the testimony of a survivor of the massacre, Chang also described a killing contest amongst a group of Japanese soldiers to determine who could kill the fastest. On the rape that occurred during the massacre, Chang wrote that "certainly it was one of the greatest mass rapes in world history." She estimated that the number of women raped ranged from 20,000 to as many as 80,000, and stated that women from all classes were raped, including Buddhist nuns. Furthermore, rape occurred in all locations and at all hours, and both very young and very old women were raped. Not even pregnant women were spared, Chang wrote, and that after gang rape, Japanese soldiers "sometimes slashed open the bellies of pregnant women and ripped out the fetuses for amusement". Not all rape victims were women, according to the book, Chinese men were sodomized and forced to perform repulsive sexual acts. Some were forced to commit incest—fathers to rape their own daughters, brothers their sisters, sons their mothers.
Chang wrote of the death toll estimates given by different sources; Chinese military specialist Liu Fang-chu proposed a figure of 430,000, officials at the Nanjing Massacre Memorial Hall and the procurator of the District Court of Nanjing in 1946 stated at least 300,000 were killed, the International Military Tribunal for the Far East (IMTFE) judges concluded that more than 260,000 people were killed, Japanese historian Fujiwara Akira approximated 200,000, John Rabe, who "never conducted a systematic count and left Nanking in February", estimated only 50,000 to 60,000, and Japanese author Ikuhiko Hata argued the number killed was between 38,000 and 42,000.
The book discussed the research of historian Sun Zhaiwei of the Jiangsu Academy of Social Sciences. In his 1990 paper, The Nanking Massacre and the Nanking Population, Sun estimated the total number of people killed at 377,400. Using Chinese burial records, he calculated that the number of dead exceeded the figure of 227,400. He then added estimates totaling 150,000 given by Japanese Imperial Army Major Ohta Hisao in a confessional report about the Japanese army's disposal efforts of dead bodies, arriving at the sum of 377,400 dead.
Chang wrote that there is "compelling evidence" that the Japanese themselves, at the time, believed that the death toll may have been as high as 300,000. She cited a message that Japan's foreign minister Kōki Hirota relayed to his contacts in Washington, DC in the first month of the massacre on January 17, 1938. The message acknowledged that "not less than three hundred thousand Chinese civilians [were] slaughtered, many cases in cold blood."