Since the existence of the complicated coupling between mould compression and resin flow, the full 3D simulation of the filling process in force-controlled compression resin transfer moulding (CRTM) has not been realized, especially when the resin flow front is irregular on the thickness direction during thick part moulding. In this paper, the coupled resin flow and mould compression behaviors are investigated firstly, a equivalent spring method is proposed to describe the preform compaction. The lubrication effect is taken into account, so the mould compression speed can be determined when the resin flow front is irregular on the thickness direction. Then the Volume of Fluid (VOF) two-phase model is established to express the resin-air flow in narrow gap and preform simultaneously, in which the narrow gap is considered as 3D area without flow resistance. Finally, the 3D numerical method for solving the above mathematical models is developed. In this method, the changing of the mould cavity is simulated by moving mesh technology, and the master-slave element method is used to simulate the resin squeezing from the infiltrated preform. Comparisons with analysis results are provided to prove the correctness of the above method, and two 3D examples are given to demonstrate the simulating capability.