The unclear understanding of the water diffusion behavior posts a big challenge to the manipulation of water absorption properties in epoxy resins. Herein, we investigated the water diffusion behavior and its relationship with molecule structures inside an epoxy resin mainly by the nonequilibrium molecular dynamics and experiments. It is found that at the initial rapid water absorption stage, bound water and free water both contribute, while at the later slow water absorption stage, free water plays a dominant role. The observed evolution of free water and bound water cannot be explained by the traditional Langmuir model. In addition, molecule polarity, free volume, and segment mobility can all influence the water diffusion process. Hence, the epoxy resin with low polarity and high molecular segment mobility is endowed with higher diffusion coefficients. The saturated water absorption content is almost dependent on the polarity. The understanding of how water diffuses and what decides the diffusion process is critical to the rational design of molecule structures for improving the water resistance in epoxy resin.