The rapid diffusion of nanoparticles (NPs) through mucus layer is critical for efficient transportation of NPs-loaded drug delivery system. To understand how the physical and surface properties of NPs affect their diffusion in mucus, we have developed a coarse-grained molecular dynamics model to study the diffusion of NPs in modeled mucus layer. Both steric obstruction and hydrodynamic interaction are included in the model capable of capturing the key characteristics of NPs' diffusion in mucus. The results show that both particle size and surface properties significantly affect the diffusivities of NPs in mucus. Furthermore, we find rodlike NPs can gain a higher diffusivity than spherical NPs with the same hydrodynamic diameter. In addition, the disturbed environment can enhance the diffusivity of NPs. Our findings can be utilized to design mucus penetrating NPs for targeted drug delivery system. (C) 2017 Published by Elsevier Ltd on behalf of Chinese Society of Theoretical and Applied Mechanics.