In order to improve the measurement accuracy of the angular error in the limited rotation axis system, the principle and method of measuring the angular error by autocollimation theodolite was used to analysis the error sources which affect the measurement result, the simulation results show that the tilt angle of the axis of the measured shaft is the main error source. Based on the accurate error model, the method to identify the misadjustment parameters and separate the introduced error by using the least squares estimation was proposed to realize the high precision measurement of angle error. The experiment was carried out with the accuracy of 2″ single-axis position turntable as tested object. The test results of conventional methods are －309.1″~428.6″, the test error is large, however, the test results of the proposed method are －0.89"~1.01"and －1.01″~0.93″, the test error is 0.70″ and 0.78″, eliminating the test error introduced by equipment misadjustment. The method has the advantages of simple equipment and simple operation, and can realize the high precision measurement the angle error of the limited rotation axis system, can solve the problem of limited rotation axis systemengineering testing problem.