Matlab/Simulink modeling and simulation method is introduced for the trajectory and motion control compute simulation of underwater vehicles. The 6 degrees of freedom spatial motion mathematical model of underwater vehicles is established based on vector modeling means. The process of building simulink model and realizing the S function are discussed in details, and the structure-compacted universal simulation model of underwater vehicles is established. The simulation results of spatial motion, maneuverability and motion control showed the validity of the established model.