Abstract: For reducing the effect of acoustic transducers' coordinate various errors on the positioning accuracy of the undersea geodetic control point, an improved joint adjustment method with between-buoy baseline constraints is proposed for GNSS/A underwater precise positioning system with the moored buoy observation system. This method takes the surface buoy and the seafloor transponder as unknown points, and the mutual ranging information between GNSS buoys as constraints. First, the mutual ranging equation is constructed by using the baseline information between the buoys, and the positions of the acoustic transducer provided by GNSS positioning are introduced into as virtual observations to form a joint function model with the underwater acoustic ranging to solve the equation. Second, in order to balance the covariance matrices of buoy position, baseline observation and acoustic observations, the variance component estimation is applied to the improved joint adjustment to accurately determine the weight matrices of three observations. Finally, simulation data was used to verify the proposed method. Experimental results show that the accuracy of seafloor transponder positioning with the proposed method can be improved by 17.5%-46.3% as compared with the conventional positioning method and 16.5%-45.8% compared with the joint adjustment method. Simulation results demonstrate that the proposed method can perform much better than other two methods.