The quality of processed workpieces is affected directly by the precision of the linear stage. Therefore, the linear displacement calibration of machine tools must be implemented before delivery and after employment for a period of time. How to perform a precise calibration with high inspection efficiency is a critical issue in the precision mechanical engineering industry. In this study, the self-developed system integrated by the measurement module based on the common path Fabry-Pérot interferometer for linear displacement and the auto-alignment module for optical axes was proposed to realize the automatic linear displacement calibration of the linear stages. The measurement performance of the developed structure was verified experimentally. With the auto-alignment module, the cosine error was reduced to 0.36 nm and the entire procedure accomplished within 75 s without the limitation of the perceived resolution of the human eye, operational experience, and the risk of misalignment and broken cable. According to the comparison of experimental results for the linear displacement, the repeatability of the proposed measurement module was less than 0.171 m. After the compensation procedure according to the linear displacement calibration, the systematic positional deviation, repeatability, and accuracy of the linear axis could be improved to 4 m, 1 m, and 5 m respectively. Hence, the calibration efficiency can be improved by 80% with the proposed compact system, which is beneficial for the linear displacement calibration of machine tools in the precision mechanical engineering industry.