This paper introduces a design scheme using mathematical simulation software for underwater vehicle control system，which can complete the research of mathematical simulation for underwater vehicle control system，the experiment of underwater vehicle hydrodynamic parameter identification and the three-dimensional visual display of actual measurement data and simulation experiment results. The software consists of four modules： underwater vehicle mathematical model and simulation model module，control algorithm module，hydrodynamic parameter identification module and graphical interface human-computer interaction module. Besides ， the configuration of simulation model is briefly introduced in this paper.