The geometric accuracy of linear axes lays a foundation for the machining accuracy of 5-axis machine tools. Although some geometric error identification and compensation approaches were developed for linear axes, the implementation efficiency and cost remain to be improved. In this paper, a novel 13-line identification method by using a laser interferometer is proposed, and the linear axes are compensated through the modification of compensation parameters in the NC system. The verification experiments are conducted through the tri-axial movement accuracy measurement and manufactured National Aerospace Standard test piece inspection, in which three circumstances, i.e., without compensation, with lead screw error compensation, and with error compensation based on the 13-line method, are compared. By using the 13-line method, the average accuracy of the tri-axial movement and test pieces are improved by 82.2 and 41.9 %, respectively, whereas the accuracy stability are improved by 77 and 46 %, respectively. Results show that the proposed identification and compensation method is effective and efficient.