In this proposed method, which is based on combination of the nonlinear Hybrid Extended Kalman Filter (HEKF) observer, Analytical and Semi-Empirical (ASE) formulas, and Computational Fluid Dynamics (CFD) simulations, all of the hydrodynamic coefficients of a REMUS AUV are estimated to simulate its motions in 6 Degrees of Freedom (6-DoF). First, Using ASE formulas along with necessary static simulations of the AUV using commercial CFD code of ANSYS CFX software, some hydrodynamic derivatives like drag, lift, and fin coefficients are obtained. Then, utilizing the dynamic simulation of the Straight-Line Test (SLT), the longitudinal added mass coefficient is derived. Finally, benefiting from the HEKF code based on the parameter identification, other unknown coefficients like added mass and damping are estimated in the MATLAB software environment. In HEKF, positions and velocities of the vehicle, which are the system output vector, are obtained from a 6-DoF dynamic maneuver in CFX. It is worth mentioning that, in the present study, the remeshing algorithm in the dynamic mesh approach is used to simulate the dynamic maneuvers of the vehicle. Results, obtained from the proposed combined method, indicate a good agreement for estimated coefficients in comparison with the available analytical and experimental values.