Under shut-in conditions in deepwater drilling, the gas invading the bottomhole ascends along the wellbore and accumulates at the wellhead, forming a high-pressure trap, challenging wellbore pressure prediction and control. The accurate prediction of bottomhole pressure is essential for well control during shut-in conditions. In this study, a new bottomhole pressure prediction model that considers wellbore storage effects was developed to address gas invasion issues during shut-in conditions in deepwater drilling. This model incorporates factors such as the wellbore elasticity, fluid compressibility, and drilling fluid filtration loss. The calculated values show good agreement with experimental values, with the average absolute and relative errors of 2.095 × 10−2 MPa and 3.71%, respectively. Meanwhile, the results indicate that the bottomhole pressure initially increases logarithmically over time and then transitions to a linear increase, and the residual flow and gas ascent significantly influence the bottomhole pressure. Finally, the effects of various parameters on the bottomhole pressure were evaluated. Larger initial pressure differential, exposed thickness, and formation permeability accelerate the increase in bottomhole pressure during residual flow stage, while smaller filter cake permeability and drilling fluid viscosity quicken its increase during gas ascent stage. Drilling fluid density affects the initial pressure and the residual flow duration. The findings of this study would provide theoretical support for well control operations in deepwater drilling.