In this study, Al/Ni multilayer powders fabricated by cold rolling were subjected to heat treatment to investigate the effects of the change in microstructure on their exothermic reaction characteristics. Heat treatment at 180 °C for 48 h caused only minor crystallite growth but significantly delayed the self-propagating exothermic reaction, suggesting that the expansion of the Al/Ni interfacial mixing layer reduced the diffusion driving force and reaction rate. Thermoreflectance (TR) measurements of powder cross sections revealed that Ni regions acted as local thermal barriers in low-pass powders, while 40-pass powders exhibited uniform phase lag distributions, indicating an improved continuity of thermal transport pathways. These findings demonstrate that the exothermic characteristics of Al/Ni multilayer powders are governed not only by crystallite size but also by nanoscale interface structure and local thermal transport uniformity. The results newly clarify that reaction retardation under heat treatment cannot be explained solely by grain growth but is strongly associated with the expansion of interfacial mixing layers and the deterioration of heat transport.