Until now, the cancer was examined by diagnosing the pathological changes of tumor. If the examination of cancer can diagnose the tumor before the cell occur the pathological changes, the cure rate of cancer will increase. This research develops a human-machine interface for hyper-spectral microscope. The hyper-spectral microscope can scan the specific area of cell and records the data of spectrum and intensity. These data is helpful to diagnose tumor. This research aims to develop a new system and a human-machine interface to control the hyper-spectral microscope. The interface can control the moving speed of motor, the exposure-time of hyper-spectrum, real-time focus, image of fluorescence, and record the data of spectral intensity and position.