As a novel effective label-free b!omarker, the mechanical properties of cells have become increasingly important. However, the current methods of mapping the cellular mechanical properties are mostly carried out manually and this results in that the measurements are time consuming, which can not meet the demand of testing a large quantity of cell samples for biological statistical analysis. In this paper, a high-speed automatic system for measuring the mechanical properties of cells based on atomic force microscopy （AFM） is proposed. In this system, cells are recognized using an image processing method and the relative position of the cell with respect to AFM tip is accurately calibrated by the local scan method, i.e., the mechanical properties of cells can be measured sequentially without performing the step of AFM imaging. Besides, with the automation implementation, the high-throughput measurement of cellular mechanical properties can be performed rapidly. Experimental results show that the measurement efficiency of our system is 27 times faster than that of the traditional method.