Abstract: Under the policy background and advocacy of carbon capture, utilization, and storage (CCUS), CO2-EOR has become a promising direction in the shale oil reservoir industry. The multi-scale pore structure distribution and fracture structure lead to complex multiphase flow, comprehensively considering multiple mechanisms is crucial for development and CO2 storage in fractured shale reservoirs. In this paper, a multi-mechanism coupled model is developed by MATLAB. Compared to the traditional Eclipse 300 and MATLAB Reservoir Simulation Toolbox (MRST), this model considers the impact of pore structure on fluid phase behavior by the modified Peng–Robinson equation of state (PR-EOS), and the effect simultaneously radiate to Maxwell–Stefan (M–S) diffusion, stress sensitivity, the nano-confinement (N-C) effect. Moreover, a modified embedded discrete fracture model (EDFM) is used to model the complex fractures, which optimizes connection types and half-transmissibility calculation approaches between non-neighboring connections (NNCs). The full implicit equation adopts the finite volume method (FVM) and Newton–Raphson iteration for discretization and solution. The model verification with the Eclipse 300 and MRST is satisfactory. The results show that the interaction between the mechanisms significantly affects the production performance and storage characteristics. The effect of molecular diffusion may be overestimated in oil-dominated (liquid-dominated) shale reservoirs. The well spacing and injection gas rate are the most crucial factors affecting the production by sensitivity analysis. Moreover, the potential gas invasion risk is mentioned. This model provides a reliable theoretical basis for CO2-EOR and sequestration in shale oil reservoirs.