Injecting CO2 into shale oil reservoirs is one of the most effective methods for enhancing oil recovery (EOR) while simultaneously facilitating CO2 capture, utilization, and storage (CCUS). However, it is not always that gas dissolution or condensate evaporation reaches equilibrium instantaneously during the CO2 injection process. In cases where equilibrium is not attained instantaneously, conventional vapor-liquid equilibrium models will have certain limitations in characterizing phase transition hysteresis. These limitations will affect the accuracy of simulating multi-component transport in porous media. In this paper, a robust and generic vapor-liquid non-equilibrium thermodynamic model considering nano-confinement effects (NC) was established by introducing component mass transfer rates proportional to the chemical potential difference. The established model was then used to modify the fully-compositional, projection-based embedded discrete fracture model (pEDFM). Furthermore, C++ hybrid programming and the Graphics Processing Unit (GPU) parallel method were both used to accelerate both the nonlinear and linear solvers. By comparing with results from MATLAB Reservoir Simulation Tools (MRST), Eclipse, and tNavigator, the accuracy and advantages of our solver were demonstrated. The results show that if the underground fluid undergoes a phase transition from a vapor-liquid two-phase state to a single-phase state, non-equilibrium thermodynamic effects need to be considered, and the simulation results show a larger two-phase zone, higher bottom hole pressure, and lower cumulative liquid production. But the nano-confinement effects will weaken the non-equilibrium thermodynamic effects.