When observing a target with a short-wave infrared microscope, the vertical size of the target is often limited by the depth of field of the lens. Aim at this problem, a multi-focus fusion method that can effectively expand the depth of field of microscope images is proposed. A large number of images with different focal planes is obtained by changing the object distance. Multiscale and local weighted variance is used to quantify the area definition. Then the focal plane mask is obtained. The morphological methods is used to optimize the mask boundary. Finally, focal plane regions are used to obtain the fusion image with complete details by weighted fusion. In the experiment, a microscope lens with a depth of field of about ten microns is used to obtain a high-quality image of a target with a vertical size of several hundred microns. The experimental results show that compared with other methods, the proposed method has certain advantages in terms of keeping the boundary of the focus plane and the details.