The simulation of three-dimensional (3D) non-isothermal, non-Newtonian fluid filling process is an extremely difficult task and remains a challenging problem, which includes polymer melt flow with free surface coupled with transient heat transfer. This paper presents a full 3D non-isothermal two-phase flow model to predict the complex flow in melt filling process, where the Cross-WLF model is applied to characterize the rheological behavior of polymer melt. The governing equations are solved using finite volume method with SIMPLEC algorithm on collocated grids and the melt front is accurately captured by a high resolution level set method. A domain extension technique is adopted to deal with the complex cavities, which greatly reduces the computational burden. To verify the validity of the developed 3D approach, the melts filling processes in two thin rectangular cavities ( one of them with a cylindrical insert) are simulated. The predicted melt front interfaces are in good agreement with the experiment and commercial software prediction. For a case with a rather complex cavity, the dynamic filling process in a hemispherical shell is successfully simulated. All of the numerical results show that the developed numerical procedure can provide a reasonable prediction for injection molding process. (C) 2016 The Chemical Industry and Engineering Society of China, and Chemical Industry Press. All rights reserved.