This paper presented the three-dimensional oocyte manipulation system for the two-electrode voltage clamp (TEVC) experiment under stereomicroscopy. We firstly developed a sequential calibration method to correlate the workspace of the stereomicroscopy with the image and the micromanipulator. Even though the focal depth of the microscopy was limited, the proposed method functioned the three-dimensional position detection and calculated the homogeneous transformation matrix. We secondly employed hybrid use of the image-based manipulation and the quartz crystal resonator (QCR) force sensor. The imaging technique was used to detect the tip of the glass capillary and the contact to the cell membrane, whereas the QCR force sensor was incorporated to detect the force interaction between the sample and the glass capillary. Using the system and proposed technique, we demonstrated the automatic capillary insertion for TEVC experiment, at which the low insertion depth was preferable. The results indicated that the coordination calibration technique provided the positioning accuracy of the capillary tip on the order of 10 μm. The imaging technique could detect the contact to the elastic objects and cell membrane. QCR force sensor achieved quite small force measurement and feedback control at the control frequency of 100 Hz without latency.