The multi-phase Darcy flow method is the most complicated among all the modeling methods for secondary hydrocarbon migration. It has three major technical problems:（1）its model is too complicated to easily generate a solution，at least much difficult than that in reservoir simulation;（2）it is not easy to ensure the convergence and stability of the model and thus rendering a calculation of low accuracy or causing abnormal shut-down; and（3）it is very time-consuming as the calculation of a larger basin may take several days to complete. To tackle these problems，we tried the finite volume method based on PEBI（perpendicular and bisection）cells，the fully implicit solution based on the Newton iteration，and the ORTHMIN（orthogonal minimum）algorithm，and came to a conclusion that the key to deal with the problems is to correctly select the allowable maximum time step for a simulated block. Finally，we developed a program of3D3-phase Darcy Flow. An application of the software to the Kuqa Depression had gained positive results.