Miscibility in chitosan/amylose blends is of great significance in research, as chitosan and starch show good complementary effects in terms of mechanical and thermal properties. In order to predict the miscibility of chitosan with starch, the Flory-Huggins parameter χ, radial distribution function of atom pair, and diffusion coefficient of the polymer chain were simulated by molecular dynamics simulation, and under the condensed-phase optimized molecular potential for atomistic simulation studies (COMPASS) force field and NPT ensemble. Results indicated that the value of parameter χ was the smallest, the bonding force of molecular chains and diffusion coefficient between amylose and chitosan chain segment were the largest when the mass ratio of amylose/chitosan was 30/70 at the same temperature when compared to the mass ratios of 70/30 and 50/50. This showed that the miscibility of the binary system (mass ratio of 30/70) was better than that of the other two systems. The addition of amylose into chitosan suppressed the mobility of chitosan chains due to a decrease in crystallization and relaxation rate of chitosan caused by amylose chain segments.