In this research, we proposed an intensity transmission type three-dimensional (3D) microscopy. The new optical microscopy is based on the critical angle method and the use of CCD detection technology to measure the 3D profile of a transparent specimen. When the beam passes through the transparent specimen, the surface height of each test point causes its output ray deflect a slight angle. Then, let the ray incident into a parallelogram prism. The incident angle deviated a small angle from the original angle is near at the critical angle, it results in a sensitive change of intensity of the reflective light. Thus the reflectivity of light is proportional to the surface height. Using a CCD camera to catch the image and using the MATLAB program to analyze the surface height, we could use the linear transform from reflectivity to height to describe the 3D profile of the specimen.