Unlike gas-assisted injection molding, subsequent penetration occurs on the radial direction after water displacing polymer melt in cavity due to the incompressibility and fast cooling of water in water-assisted injection molding. To simulate this second penetration, a dimensionless method was employed to simplify, the governing equations jar melt flow. Based on the reduced model, a formula was derived via mathematical inference to calculate the second penetration velocity and distance. In order to catch the huge temperature gradient at water-polymer interface, both polymer and water thermal conduct problems were founded and coupled at the interface. The finite element method was employed to solve the melt flow problem, and the finite difference method was used to discretize the energy, equation. To verify the validity of the proposed model and algorithm, experiments were performed to measure the displacement of the water-melt interface fir various melt temperatures and water pressures. The experimental results indicate that the primary penetration theory is not accurately on predicting residual wall thickness, whereas the combined primary and second penetration method significantly improve the accuracy.