In this paper, a new cell micro-injection system with stereo vision is proposed to guide the cell injection operation. The depth detection problem in the cell injection system is solved with dual-camera stereo vision. The 3-D visual servoing system is realized in order to locate the targets in stereo space, which will simplify the injection operation directly. An upgraded template matching algorithm and the color thresholding method are applied to locate the injector and cells, respectively. Experimental result show that the developed system can locate the injector and cell with precise solution, and the locating resolution is 1.752 μm. A PID position control is realized for the system to minimize the motion tracking error. Meanwhile, the cell size is measured to feedback its deformation in piercing process, which serves as the indication of puncturing successful signal. Experimental results validate the effectiveness of the developed stereo cell micro-injection system.