Flow induced stress and molecular orientation formed in melt filling stage will be frozen or partially frozen in the injected plastic parts, and influence its final mechanical properties to a great extent. The aim of this work is to investigate polymer macromolecular orientation and flow induced stress for the filling stage in rapid heat cycle molding process. Mathematical model and numerical implementation are presented for the three-dimensional non-isothermal viscoelastic flow problem for the polymer melt were presented. The Double Convected Pom-Pom constitutive model (DCPP) was used to describe the thermal viscoelastic behavior of the polymer melt. Temperature distribution on the electrical heated mold cavity was analyzed and employed as boundary condition during melt filling simulation. Effects of processing parameters, including injection temperature, injection rate, mold temperature and cavity thickness, on the molecular orientation and flow induced stress for melt filling flow in an electrically heated rectangle mold cavity were numerically studied. The results show that the normal stress increases quickly with the distance to the cavity center, and decreases to a certain extent after a maximum is reached near the cavity wall. The predicted birefringence profiles, representing the orientation degree of the macromolecular, exist a maximum near the cavity wall. The thinner the cavity is, the bigger the maximum is. This max birefringence index decreases with the increasing of flow rate and injection temperature. While the influence of mold temperature on the birefringence is not very pronounced. These numerical results will be verified with the forthcoming experiments. The presented mathematical model and numerical results provide useful information to predict the quality of plastic parts in rapid heat cycle molding technology.