Molecular dynamics simulations is performed to study the diffusion of several short alkanes in a flexible and rigid metal-organic framework, IRMOF-1. The results show that the self-diffusivities of alkanes in the flexible framework are larger than in a rigid framework and the activation energies in the flexible framework are less than in the rigid framework. The effect of framework flexibility on the self-diffusiviy increases with temperature inereasing and loading or chain length decreasing. Therefore, in the study of the diffusion behavior of alkanes in the metal-organic framework materials using molecular simulation method, especially for the case of the high temperature and shorter alkane molecules, flexible force field may give more reasonable results.