Reducing graphene oxide suspension with amino agent can prepare N-containing graphene aerogels useful in many applications. This work studied the reaction process during the synthesis of N-doped graphene aerogels (NDGA) with p-phenylene diamine (PPD) as reducing and functionalizing agent based on the experimental and calculated results. The amino group in the PPD firstly reacts with the hydroxyl in the carboxyl for the strong electron-donating effect of carbonyl. Then the reaction happens between the amino group and the epoxy group. This reaction not only induces the forming of the pyrrolic N, but also changes the interlayer distance. The reaction process ideally explains the reasons for the structure and composition change during synthesis. This work provides a more thorough understanding of the reaction process during the synthesis of NDGA, which is significant for the optimization of the aerogels. And these findings are also useful for understanding the reaction process and reaction mechanisms during the synthesis of reduced graphene oxide aerogels with other amino agent as reductant.