In view of the problem that the previous ship ballast water simulation system can only be used for certain specific ships, the parametric modeling method based on the pipe network finite element method is proposed. In order to realize the optimization of ballast water regulating scheme, the automatic regulating algorithm based on Non-dominated Sorting Genetic Algorithm Ⅱ (NSGA-Ⅱ) and the regulating scheme search method based on Back Propagation (BP) Neuron Network are added to the simulation system. A ship ballast water simulation system is developed by the hybrid programming methods such as C#, MATLAB, Structured Query Language (SQL), etc. The application in different ships shows that the system possesses the generality and can automatically generate the reasonable regulating scheme according to the target.