A transmission stereo microscope is presented based on programmable light emitting diode（LED） array illumination so as to realize stereo imaging with high quality. The programmable LED array is the illumination source of this optical system. The radius, angle and wavelength of illumination can be chosen freely. The depth of focus and the stereotype angle can be adjusted by changing r and d of the programmable LED array at will. Experimental results show that the microscope system is simple, and double images which can not be coincided owning to the difference of individual pupil distance can be solved effectively by choosing appropriate r and d. The stereo image of samples can be obtained in details directly. The three-dimensional information such as hierarchy and relative position can be observed with optimal parameters r=2 and d=3 by using objective NA=0.1(4×).