In this paper, a specially designed three dimensional transient heat transfer model has been developed for initial stage of steel continuous casting process. Firstly, a general three dimensional heat transfer model for continuous casting process has been established, and it is discretized by finite volume method and solved by alternative direction implicit method. For transient simulation of initial stage, the fixed-length moving bloom with dummy bar at its bottom experiences time-variant boundary conditions, while the filling process is also equivalent to moving process. Secondly, the transient model has been calibrated by surface temperature measurements by pyrometer and shell-thickness measurements by nail-shooting.Online temperature measurement for verification indicates the calibrated model is reliable as the maximum error between calculations and measurements are within ±28℃, and soon in less than 80s the error will be reduced to within ±5℃. Thirdly, uncertainty caused by dummy bar's length and thermo-physical properties has been studied, and the results indicate that the uncertainty is quite small and acceptable. Finally, the model has been applied to optimizing the secondary cooling water flows and cut length of strand head.