The secondary-phase grating-based tomographic microscopy system, which is widely used in the biological and life sciences, can observe all the sample multilayer image information simultaneously because it has multifocal points. However, chromatic aberration exists in the grating diffraction, which seriously affects the observation of the image. To correct the chromatic aberration of the tomographic microscope system, this paper proposes a system that adopts blazed gratings and angle-variable reflectors as chromatic aberration correction devices according to the principle of dispersion compensation and Fourier phase-shift theory. A reflector-separated light dispersion-compensated 3D microscopy system is presented to achieve chromatic aberration correction while solving the problem of multilayer image overlap. The theoretical verification and optical design of the system were completed using ZEMAX software. The results show that the proposed system reduced the chromatic aberration of ordinary tomographic microscopy systems by more than 90%, retaining more wavelengths of light information. In addition, the system had a relatively wide range in the color difference compensation element installation position, reducing the difficulty of dispersion compensation element installation. Overall, the results indicate that the proposed system is effective in reducing chromatic aberration in grating diffraction.