Aiming at the great error of positioning and measurement of a shipborne theodolite caused by vessel shaking, a high precision solution for correcting the vessel-shake error is proposed. Vessel-shake attitude angel and GPS local baseline positing information are measured by an inertial navigation system. The shipborne theodolite data of real-time position and measuring angle are performed to vessel-shake error correction. And the influence on measuring angle accuracy from position error is researched. According to the data error comparison analysis before and after correction, the exterior trajectory measuring accuracy of sea-based measurement and control equipments is improved. Experimental results show that the method is simple and applicable. The corrected accuracy can meet the requirements, and can be applied widely.