Understanding the intermetallic reaction is critical for reactive metal systems, among which Ni/Al nanolaminates have attracted extensive interest. A long-standing open question is how nanostructure such as premixed interlayer affects the reaction process. Here, we employ molecular dynamics simulations to investigate the effects of premixing degree on the shock-induced reaction mechanisms and reactivity for premixed Ni/Al nanolaminates. The multiple exothermic processes are identified, namely, the Ni–Al mixing driven by diffusion, the B2-NiAl crystallization in premixed interlayer, and the grain coarsening driven by grain boundary migration. Intriguingly, it is found that the specific exothermic processes depend strongly on the premixing degree. As the premixing degree increases, the B2-NiAl crystallization and the grain coarsening appear sequentially. The maximum crystallinity and grain size increase linearly and exponentially with premixing degree, respectively. Furthermore, inspired by the differences in exothermic processes, the intrinsic mechanism for the weakening effects of premixed interlayer on reactivity is elucidated. The B2-NiAl crystallization in premixed interlayer decreases the reaction heat and further the final adiabatic temperature, while the appearance of grain coarsening produces additional heat and alleviates the weakening effect. These findings can provide valuable insights into the nanostructure–reactivity relationship for reactive intermetallic materials.