Based on the theories and methods of system engineering, the reconstruction of physical space for oil and gas generation, expulsion, migration, accumulation and diffusion is realised by combining the dynamics simulation with topological structure simulation and applying the topological structure simulation. The integral non-linear process of petroleum system is described successfully with the combination of general and system dynamic simulation. The integration of numerical simulation and artificial intelligence simulation solves the non-linear process description of petroleum generation, expulsion, migration, accumulation and diffusion. At the same time, the basin geological body and its oil and gas generation, expulsion, migration, accumulation process of the three-dimensional visualisation of dynamic modelling, spatial analysis and trap evaluation technologies were further developed in this system. The software has been applied successfully in modelling petroleum systems of Tarim River Oilfield, Zhu III Depression, Linqing Depression, Baise Basin and Dongying Depression, China.