In the external damping system, the external velocity error has direct influence on the alignment result of the gyrocompassing loop. Based on the characteristics of the gyrocompassing loop,this manuscript deduces the effect of different kinds of sea current velocities to the alignment result in theory, which is further verified and analyzed through simulation. Since the sea current velocity satisfies some mathematical model in a specific sea area, it is possible to be measured and modeled before applied to the damping system for the compensation purpose. Therefore, a current velocity calculation method is introduced by directly comparing the velocity estimated in GNSS/INS integration to the velocimeter's output. The sea current velocity model is formulated, which is based on the calculation result. During the gyrocompassing process, the velocity model is further used to compensate the velocimeter's output in the specific area. The marine experimental results show the effectiveness of the proposed method on improving the attitude accuracy and convergence speed. The horizontal attitude accuracy is improved by 36", and the yaw angle is improved by 25". The horizontal convergence speed is improved by 25 minutes.