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The dual-color multi-channel fiber optic recording system adds a 405nm purple control channel on the basis of the original multi-channel fiber optic recording system. The data of this channel can be recorded as control data to eliminate the noise interference of the recording channel. The two wavelengths of excitation light are coupled to the same optical fiber through the optical path and transmitted to the specific brain area of ​​the experimental animal. The fluorescence of the calcium signal returned by each channel is then transmitted back to the processing optical path through the optical fiber. The system adopts the time division multiplexing method and CMOS area array imaging method to collect the fluorescence brightness excited by the two excitation lights of each optical fiber in the multimode fiber bundle in real time, thereby realizing the synchronous recording of multiple channels.