Compared with the current multi-step method to solve the coordinate of the transponder, the combined solution of GNSS observation data and acoustic observation data is more consistent with the actual operation state, but if the error of attitude angle cannot be eliminated in the process of coordinate transformation, the accuracy of the transponder positioning will be seriously affected. Aiming at this shortcoming, based on the proposed GNSS/ acoustic joint positioning model in this paper, the attitude angle is used as the parameter to be estimated to participate in the filtering solution, and the filtering effect of the new model is verified by simulation and experimental data in this paper. The results show that: after the attitude parameters’ adding into the filtering model for estimation, the results of the three-dimensional coordinate error of the transponder are improved in varying degrees, and when the range of attitude error is larger, the improvement effect is more obvious.