Warpage is a typical defect for injection-molded parts, especially for crystalline parts molded by rapid heat cycle molding (RHCM). In this paper, a prediction method is proposed for predicting the warpage of crystalline parts molded by the RHCM process. Multi-layer models were established to predict warpage with the same thicknesses as the skin-core structures in the molded parts. Warpages were defined as the deformations calculated by the multi-layer models. The deformations were solved using the classical laminated plate theory by Abaqus. A model was introduced to describe the elastic modulus with the influence of temperature and crystallinity. The simulation process was divided into two procedures, before ejection and after ejection. Thermal stresses and thermal strains were simulated, respectively, in the procedure before ejection and after ejection. The prediction results were compared with the experimental results, which showed that the average errors between predicted warpage and average experimental warpage are, respectively, 7.0%, 3.5%, and 4.4% in conventional injection molding (CIM), in RHCM under a 60 °C heating mold (RHCM60), and in RHCM under a 90 °C heating mold (RHCM90).