To ensure the angle measuring accuracy of a shipboard theodolite, and to compensate the errors of the station position and ship-swaying measurement, the effect of attitude data on angle measuring errors was analyzed and a ship-swaying error model was established. On the basis of the model, a scheme for calibrating and measuring the equipment was given, and then a shipboard stations position correcting algorithm and data post-processing method were proposed. First, the ship-swaying error model was build, and the formulas for the effects of measuring errors from the ship′s head, pitch and the roll on measured azimuth and elevation angles of the equipment were given. Combined with the equipment indicators and mission requirements, a scheme for calibrating and measuring was established and the measured angle ranges to ensure the accuracy of the equipment were given. Furthermore, a measuring method of station position and its correcting method were proposed when the equipment works at special working environments. Finally, a data post-processing method for shipboard equipment was explained. Experimental results show that the Root Mean Square(RMS) of angle measuring errors of the equipment are less than 57″ for the azimuth, less than 34" for the pitch when the shipboard accurate attitude measurement system has angle measuring errors at the head of 1.2', pitch of 24″ and the roll of 24″, respectively. The result has basically reached the optimal theoretical accuracy under this measurement conditions.