As a novel effective label-free biomarker, the mechanical properties of cells have become increasingly important. However, the current methods of mapping cellular mechanical properties are mostly carried out manually, resulting in measurements that are time-consuming with low efficiency. In this article, a fully automated system of measuring the mechanical properties of cells based on atomic force microscopy (AFM) is proposed. In this system, the cells are recognized using an image-processing method and the relative position of the cell, and the AFM tip is accurately calibrated by the local scan method, meaning that the mechanical properties of cells can be measured sequentially without performing the step of AFM imaging. In addition, with the implementation of the automation, the high-throughput measurement of cellular mechanical properties can be performed rapidly. The capability of our system is validated on Raji cells, and the results indicate that the measurement rate of our system is 26 times faster than that of the traditional manual method, providing the technology for high-throughput measurement of cellular mechanical properties.