A coupled mathematical system of four quasi-linear partial differential equations and the initial-boundary value conditions is presented to interpret transient behavior of three dimensional semiconductor device with heat conduction. The electric potential is defined by an elliptic equation, the electron and hole concentrations are determined by convection-dominated diffusion equations and the temperature is interpreted by a heat conduction equation. A mixed finite element approximation is used to get the electric field potential and one order of computational accuracy is improved. Two concentration equations and the heat conduction equation are solved by a fractional step scheme modified by a second-order upwind difference method, which can overcome numerical oscillation, dispersion and computational complexity. This changes the computation of a three dimensional problem into three successive computations of one-dimensional problem where the method of speedup is used and the computational work is greatly shortened. An optimal second-order error estimate in $L^2$ norm is derived by prior estimate theory and other special techniques of partial differential equations. This type of parallel method is important in numerical analysis and is the most valuable in numerical application of semiconductor device and it can successfully solve this international famous problem.