Error compensation technology as an economical and effective method for improving the machining accuracy of the machine tools has been widely applied in the manufacturing. How to quickly and accurately obtain machine tool error is an important prerequisite for achieving the above task. A laser tracker is adopted the multi-station and time-sharing measurement principle to achieve quick and accurate identification of the geometric errors of the machine tool. In this article, the error of single-station measurement of laser tracker is analyzed first, and then the principle and algorithm of multi-station and time-sharing measurement are given. Based on the kinematic model of the machine tool, the mapping relation equations between the space motion error and individual geometric error of the machine tool are established, and two different identification algorithms are derived, respectively. Meanwhile, the identification accuracy of two algorithms and the impact of different measurement areas and squareness errors on two algorithms are compared and analyzed in depth. The experiment results indicate that higher identification accuracy can be obtained by the second algorithm, and individual geometric error of the machine tool can be quickly and accurately separated by this algorithm.