An auto-microimaging system to provide 3D scanning and auto-focus at each dimension was designed for the high throughput micro-imaging of drug screening. The mechanical structure, man-machine interaction software, the section of focusing evaluation function and the image titching of multi-view image for the system were researched. A rack structure was designed to overcome the limitation of accuracy from the deformation and a servo motor and a voice coil motor were combined as a two-stage controller to improve the accuracy and focus speed of the measuring system. Then, an algorithm of auto-focus was presented after several auto-focus evaluating methods were compared. According to the effect of a small view under the high power microscope on the experimental statistics, the function of image stitching was designed to fit the statistical significance of the experiment. On the experimental verification, it indicates that the time to complete the process of auto-focus is 2 s, and the accuracy of auto-focus can reach several micrometers. Moreover, the time to combine the micro-imaging regions of a 4×4 array is 15 s. The system can satisfy the requirements of short detection time, robotization, stability and reliability of cell analyzing with multiple well plates in drug screening.