Fluid flow in tight gas reservoirs with abnormal high pressure presents nonlinear behaviors. A mathematical description of these behaviors is essential for establishing the flow model. In this study, a mathematical model is presented that describes the effect of threshold pressure gradient and rock deformation on gas flow parameters in a tight gas reservoir. A fully implicit 3D gas and water phase numerical model was derived using the finite difference method. Based on software engineering principles, a 3D gas and water simulator was developed, which can be used in research on nonlinear flow mechanisms and flow simulation in abnormal high-pressure gas reservoir. The simulator proved to be reliable through a comparison with a commercial simulator, and it was used successfully for prediction of gas production in the M reservoir.