The intrinsic properties of the observed object are closely related to its spectral information, to extend the imaging spectral range of a continuous zoom microscope to obtain more detailed intrinsic properties of the object, this paper proposes a design method of dual-band simultaneous zoom microscope optical system based on the coaxial Koehler uniform illumination. First, the imaging principle of the dual-band simultaneous zoom microscope optical system is theoretically analyzed, and we propose to split the front fixed group of the zoom system into a collimation lens group and a converging lens group to realize the compact design of the system. Then, two different rear fixed groups are used to correct the residual aberration, and a method for solving the initial structure of the dual-band simultaneous zoom microscope optical system is proposed. Finally, a dual-band synchronous zoom microscope optical system is designed using the method proposed in this paper. The design results show that the imaging magnification of the visible (VIS) band is −0.4 to −4.0, the simultaneous imaging magnification ranges are −0.4 to −0.8 in the VIS and short-wave infrared (SWIR) bands, and the magnification difference of its simultaneous zoom imaging is less than 1.25%. In addition, the system has the advantages of good imaging quality, clever design of coaxial illumination, and compact structure, thus verifying the feasibility of the design method.