This paper presents a monocular biological microscope with colorful 3D reconstruction and an extended depth of field using an electrically tunable lens. It is based on a 4f optical system with an electrically tunable lens at the confocal plane. Rapid and extensive depth scanning while maintaining consistent magnification without mechanical movement is achieved. We propose an improved Laplacian operator that considers pixels in diagonal directions to provide enhanced fusion effects and obtain more details of the object. Accurate 3D reconstruction is achieved using the shape-from-focus method by tuning the focal power of the electrically tunable lens. We validate the proposed method by performing experiments on biological samples. The 3D reconstructed images obtained from the biological samples match the actual shrimp larvae and bee antenna samples. Two standard gauge blocks are used to evaluate the 3D reconstruction performance of the proposed method. The experimental results show that the extended depth of fields are 120 µm, 240 µm, and 1440 µm for shrimp larvae, bee tentacle samples, and gauge blocks, respectively. The maximum absolute errors are −39.9 μm and −30.6 μm for the first and second gauge blocks, which indicates 3D reconstruction deviations are 0.78% and 1.52%, respectively. Since the procedure does not require any custom hardware, it can be used to transform a biological microscope into one that effectively extends the depth of field and achieves highly accurate 3D reconstruction results, as long as the requirements are met. Such a microscope presents a broad range of applications, such as biological detection and microbiological diagnosis, where colorful 3D reconstruction and an extended depth of field are critical.