Abstract: In view of the characteristics of autonomous underwater navigation(terrain-aided one) system,a series of data pretreatment,algorithm analysis,performance evaluation and intelligent data fusion are dealt with,which comes form the geographical characteristics of ocean sensors.Then the simulation design of autonomous underwater navigation system is finished.These work provided the feasible design project and technological ideas for the further research of underwater autonomous navigation system.According to the simulation results,the assistant navigation with underwater terrain matching can amend the errors of inertial navigation effectively and its main goals of the design are achieved.In this way,accurate navigation in the actual ocean will be located on its reliable technology-the underwater navigation matching with terrain #aided one.