Diffusion and seepage collectively govern the mass transfer behavior of gases in the CO2 enhancing coalbed methane recovery (CO2-ECBM) process, significantly influencing both coalbed methane extraction efficiency and CO2 sequestration capacity. Conventional theoretical models typically assume a uniform gas distribution within the coal matrix during injection. However, extensive field studies have revealed inconsistent conclusions. This paper delves into the gas equilibrium time lag property during the CO2-ECBM process, introducing the concept of sub-matrix mass transfer behavior to describe the non-uniform distribution of pressure, and construct the modified binary gas flow control equations and the permeability evolution model that takes this behavior into account. This model is used to investigate how sub-matrix mass transfer influences gas seepage characteristics. Findings show that the equilibrium time lag property intensify with coalbed extension but diminish over time. Despite an increased sub-matrix proportion enhancing CO2 adsorption capacity, the difference fades away due to the decay of the gas equilibrium time lag property. Furthermore, fixed-point monitoring reveals that a higher sub-matrix proportion aggravates permeability evolution, constraining fluid flow capacity. Based on these observations, a hypothesis of multi-level diffusion behavior within the coalbed is proposed, alongside an exploration of optimized CO2 injection strategies, providing new theoretical insights for CO2 sequestration in deep coalbeds.