The work aims to conduct molecular dynamics simulation to investigate the diffusion mechanisms of thymol (THY) and carvacrol (CAR) in polypropylene (PP) active packaging materials. The unit cell models of isotactic, syndiotactic and atactic PP matrices including THY and CAR were established to study the diffusion behaviors of THY and CAR from the perspective of mean squared displacement and the diffusion mechanisms of THY and CAR were explored from encompassing solubility parameters, interaction energies, movement trajectories, and free volume. The results showed an increase in the fraction of free volume (FFV) of the unit cells, an enhancement in the diffusion coefficients and an expansion of the movement trajectories of THY and CAR with the increase of temperature, facilitating the transformation from a single cluster to multiple clusters. When the THY and CAR were in various PP matrices, the diffusion coefficients of them decreased as the crystallinity increasing, whereas the FFV of the unit cells raised with higher crystallinity. While when they were in the same matrices, PP had a better compatibility with THY than CAR, and the FFV of THY unit cell was smaller than that of the CAR unit cell. Additionally, the interaction energies of THY, CAR and PP did not differ much and the interaction energy was almost contributed by van der Waals forces. Thus, it can be concluded that the diffusion of active agents in packaging materials is influenced by multiple factors, including temperature, the structure of the active agent, the structure of the material, and the compatibility between the active agent and the material, and temperature can remarkably influence the diffusion while the other factors exhibit insignificant effect.