In recent years, neuroscientists have become more and more interested in brain imaging of conscious and free-behaving animals, hoping to obtain nerve impulse signals in the brains of free-behaving experimental animals, especially certain types of cellular activity may be inhibited by anesthesia. Combined with the Genetically Encoded Calcium Indicator (GECI), the miniature microscope has the ability to image the brain of free-behaving animals and obtain the signal of nerve impulse. The miniature microscope is then widely used in the study of brain science. Currently, most optical systems of miniature microscopes are limited by chromatic aberration due to the use of Gradient Index Lenses (GRIN), which does not meet the experimental requirement of the two-color fluorescent imaging effect. Dual-color fluorescence imaging miniature microscopes have a number of advantages, such as the ability to compare the activities of two different cell populations in the same brain region of a free-behaving animal combined with GECIs which have distinguishable color spectrums, or it can be used for the motion correction. Therefore, a Dual-color Fluorescent Imaging Miniature Microscope (DCFIMM) is developed. Firstly, in order to enhance the dual-color fluorescent imaging capability of the miniature microscope, a micro achromatic lens is designed to replace the gradient index lens. The miniature achromatic lens is composed of double cemented lenses, which forms an infinity correction optical system with the imaging lens. And according to the application direction of cerebral cortex imaging and deep brain imaging, DCFIMM-SBI (superficial brain imaging) and DCFIMM-DBI (deep brain imaging) are designed, both have a larger imaging field of view than the monochromatic fluorescence imaging miniature microscope with grin lens, which are 1.10 mm×1.10 mm and 0.77 mm×0.77 mm respectively. Meanwhile, the dual-band filter for green and near-infrared is used to reduce fluorescent crosstalk. Secondly, a data acquisition circuit is designed to alternately trigger two LEDs with different wavelengths with the frame rate of the CMOS camera. Therefore, the green fluorescent information and near-infrared fluorescent information can be obtained in odd-numbered frames and even-numbered frames, respectively. Our system can realize the imaging speed of 10 fps with the ability of dual-color fluorescence imaging. Thirdly, the video data is stored in a micro SD card. DCFIMM is not limited by the wire transmission. Finally, the structure design of our DCFIMM is optimized. The whole weight of our DCFIMM is 4.8 g (6.2 g with a battery). The experimental results of the USAF 1951 high-resolution target show that the achievable resolution of our DCFIMM is 3.47 μm, which is comparable with monochromatic fluorescent imaging using a miniature microscope with GRIN lens. In the dual-color fluorescent imaging experiment for the hybrid microsphere, DCFIMM can distinguish the fluorescent microspheres of different colors. Compared with the experimental results of monochromatic fluorescence imaging miniature microscope with grin lens, it is found that the chromatic aberration of the DCFIMM optical system has also been well corrected, which demonstrates that our DCFIMM has the ability to distinguish fluorescence of different wavelengths. The proposed DCFIMM in this paper shows promising and wide applications for brain science research.