In order to simulate quickly and accurately the magnetic anomaly caused by ship wake，the author built the mathematical model of wake magnetic anomaly based on the theory of Maxwell equation，magnetic fluid dynamics and ship hull correlation theory，and designed the simulation system for wake magnetic anomaly by using the guide tool of MATLAB software. The size and spatial distribution of wake magnetic anomalies in the course of ship motion are simulated by a designed system. We gained that the wake of magnetic anomaly in 2 - D and 3 - D space gradually wanes along the propagation direction of the distance. What’s more，the attenuation degree is related to the parameter of ship type，speed and inclination. This simulation system is easy to operate and integrates variable parameters. Besides，the simulation results are intuitive and can be repeatedly simulated，thus it is convenient for a real - time，fast and accurate simulation of wake magnetic anomalies.