This paper proposes an efficient measurement system for the velocity and direction of the wind using the dual rotor wind power generator in vessel. Conventional digital measurement system recognizes the direction and the velocity of the wind using the electric compass or synchronous motor and Vane probe method using hall sensors. But each system has its own short-comings: the synchronous motor has a larger measurement error than the magnetic compass and magnetic compass is weak for the external disturbances such as fluctuation of the vessel. To compensate these short-comings, this paper proposes a new compensation algorithm for the fluctuation errors according to the external interference and the unexpected movement of the vessel along the roll and pitch directions. The proposed system is implemented with the dual compasses and a synchronous motor. The proposed independent power generation system can be operated by itself and can raise the efficiency of the wind power generation systems of 30 ~ 400 W installed along the vertical and horizontal axes. The proposed system also realizes the efficient and reliable power production system by the MPPT algorithm for the real-time recognition of the wind direction and velocity. An advanced switching algorithm for the battery charging system has been also proposed. Effectiveness of the proposed algorithm has been verified through the real experiments and the results are demonstrated.