A homogenous phase change model (HPCM) based on the mass conservation law is proposed to analyze the flow field of a two-phase mechanical seal with 3D face structures. The two-phase flow domain is governed by the simultaneous partial differential equation set containing a mass transfer governing equation for each phase with a source term derived from the Rayleigh–Plesset model and a Reynolds equation for the mixture, where the pressure and the liquid fraction are unknowns. A numerical solution is developed based on finite element method (FEM). The results from the present model are in good agreement with those from the previous two-phase mechanical seal models. A two-phase mechanical seal with wavy-tilt-dam face structure is calculated. The results indicate that the 3D face structure affects the phase distribution by altering the film pressure field. The present model is especially useful to analyze the two-phase film flow field bounded by the complex solid surfaces.