Helium, as a probe gas with low adsorption capacity, is widely used for measuring porosity, permeability, and specific surface area in reservoir rocks of unconventional gas such as shale and coal. The pretreatment duration of these rock samples determines the amount of residual nitrogen in their pores, and the competitive adsorption and diffusion of residual nitrogen with the probe gas has a significant impact on the measurement results of their physical properties. This work aims to reveal the mechanisms involved in the competitive adsorption-diffusion coupling process of nitrogen-helium mixtures. Brief experiments were conducted to demonstrate the competitive adsorption between nitrogen and helium in shale. Subsequently, molecular dynamics simulation was employed to investigate this process and provide necessary details. Meanwhile, a theoretical model was developed to describe the diffusion of gas molecules in this process. Our results indicate that helium rapidly permeates shale samples and reaches an equilibrium distribution. However, the competitive adsorption between nitrogen and helium can slow down the helium permeation process, which can be attributed to the main adsorption sites occupied by nitrogen. The agreement between FEM computations and MD simulations validates our model for various mechanisms. Furthermore, our model can be applied to a wider range of porous materials and gas mixtures in related fields.