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The Deep-sea Autonomous Profile Buoys (DSAPB) are a new type of underwater buoys and they can dive to the deep sea below 4000m. Considering dynamic models of conventional underwater vehicle could not adequately satisfy the motion characteristic of DSAPB, a nonlinear dynamic model for the motion simulation of DSAPB is developed in this paper. In the model, the effect of sea water density change is taken into consideration and a viscous hydrodynamic calculation method satisfying the motion characteristic of DSAPB. The buoyancy variation is introduced into the standard hydrodynamic equation to simplify the DSAPB hydrodynamic equation, and the Motion of Planar Mechanisms (PMM) experiment is simulated by means of Computer Fluids Dynamics (CFD). The hydrodynamic coefficients in the equation are obtained and the DSAPB dynamic model is obtained which provides theoretical basis for effective control of DSAPB.