In CO2 geological storage, multiphase flow plays a vital role in the movement and distribution of CO2. However, due to the limitations of fluid buoyancy and capillary forces, CO2 encounters challenges in penetrating the caprock, and the potential for leakage remains a concern due to variations in injection conditions. The migration and distribution of CO2 in the process of CO2 geological storage in saline formations are determined by relative permeability and capillary pressure, which are key factors. Consequently, this study focuses on two essential models: relative permeability and capillary pressure models. A two-dimensional isothermal reservoir–caprock model was constructed, utilizing data from the Shenhua CCS demonstration project. The analysis indicates that the core parameters in the model are residual gas saturation and residual water saturation. Specifically, residual gas saturation governs the diffusion distance of CO2 within the reservoir–caprock system, while its combined effect with residual water saturation affects the permeation rate of CO2. Through the application of the Analytic Hierarchy Process (AHP) to analyze the impact of different models on caprock integrity, it was determined that when selecting caprock models and optimizing parameters, precedence should be given to models with lower residual saturation and caprocks that offer sufficient capillary pressure for optimal sealing effects. These research findings can serve as references for practical CO2 storage projects, providing guidance on activities such as adjusting water injection strategies and controlling gas injection pressures to optimize geological storage efficiency.