In general, the network structure formed in epoxy resins is heterogeneous, and its extent is dependent on the curing temperature. Based on Fourier-transform infrared spectroscopy in conjunction with coarse-grained molecular dynamics simulations, we herein discuss the origin of mesoscopic heterogeneity in an epoxy resin composed of a typical epoxy base and diamine hardener, which react with each other in two steps. The rate balance of the first and second step reactions, which led to chain extension and branching, respectively, depended on the curing temperature; at a higher temperature, the second-step reaction became faster. Since the reaction proceeded more slowly at lower temperatures, a homogeneous domain was formed as unreacted substances were incorporated into the network. At higher temperatures, on the other hand, the reaction proceeded rapidly before unreacted substances were incorporated into the network, leaving isolated small fragments and nanoscale voids or free spaces in the domain. We also found that an actively reacting domain with a length scale of several tens of nanometers was formed even at a conversion lower than the gel point, regardless of the curing temperature. The connection of domains was also key to better understanding the temperature dependence of the hierarchical heterogeneity. The final network was found to be denser and more homogeneous at a lower temperature, while heterogeneous with many free spaces at a higher temperature. Our molecular picture of the network formation drawn by combining experimental and simulation techniques advances our current understanding of the heterogeneity formed in epoxy resins.