Computer simulation for evolutionary history of an oil-gas bearing basin is to repeat its geological and thermodynamic evolutionary history on a computer. The mathematical model of basin simulation is characterised by an initial-boundary value problem of nonlinear partial differential equations on the abnormal pressure and the paleo-temperature of the formation. In the present paper, numerical method for three-dimensional proposed, the analysis on their stability and a numerical result for a practical model is given also. The results show that the abnormal pressure and the paleo-temperature computed are reasonable and display physical characteristics clearly as well.