The inverse analysis method is applied in the evaluation of heat flux at the interface between the molten polymer and the mold during the injection molding process. In addition, the dependence of cooling behavior on both the molding conditions and the material properties of the resin are investigated. During low-velocity polymer flow in the thick regions of the mold cavity, the heat flux in the later stage of the process evaluated through experiment correlates well with the theoretical results of equations describing heat conduction at the interface of two semi-infinite objects. In contrast, in the thin region of the mold cavity, the analyzed heat flux is greater than the theoretical result for high-velocity polymer flow, and the difference expands with an increase in the shear rate at the wall of the mold. Based on these results, a simple empirical equation applicable to a wide range of molding conditions is proposed for the estimation of heat flux at the polymer-mold interface.