Abstract: On the basis of analyzing the interrelationship of the complex physical and chemical phenomena in the composite cure process，a three-dimensional (3D) finite element analysis ( FEA) model was developed for simulating the process and predicting the process-induced deformation. By an integrated sub-model approach，the cure process was divided into three relatively independent modules：thermo-chemical，flow-compaction and stress-deformation. The thermo-chemical module was based on the Fourier’s heat conduction and cure kinetics equation with the consideration of the coupling relation between temperature and cure degree. In the flow-compaction module，Darcy law and effective stress principle were employed to describe the interaction between resin viscous flow and fiber bed consolidation. In the stress-deformation module，multi-layer complex composite laminates subjected to thermal load and resin cure shrinkage were analyzed by the 3D finite element method. Which module and its subroutines should be called was determined by resin gelation and vitrification. The interaction of these three modules is realized through exchanging the data between them. The representative structure simulation comparison with experiment verified the 3D FEA model in this paper.