The injection over-molding process combines thermo-stamping of continuous fiber reinforced thermoplastic (CFRTP) laminates and injection of plastic onto the surface of the CFRTP insert. A challenge for this process is to predict the warpage due to the influence of CFRTP insert. This work proposed a simulation method for predicting the warpage considering yarn reorientation induced in the thermo-stamping. In detail, the geometry and yarns reorientation of the deformed CFRTP inserts in thermo-stamping were calculated by a hybrid lamination model. Then the local thermo-mechanical properties were calculated according to the directions of reorientated yarns. Finally, the geometric and material information of CFRTP insert were imported into injection analysis, especially warpage prediction. The simulation method was validated by experiments on centrally injected bilayer plate and stiffened square box. This work highlights the importance of anisotropy induced from thermo-stamping on the final warpage of injection over-molded composite parts.