This paper presents a method for reconstructing 3D image from multi-focus microscopic images captured with different focuses. We model the multi-focus imaging by a microscopy and produce the 3D image of a target object based on the model. The 3D image reconstruction is done by minimizing the difference between the observed images and the simulated images generated by the imaging model. Simulation and experimental result shows that the proposed method can generate the 3D image of a transparent object efficiently and reliably.