The optical fiber photometry system with optogenetic function makes the optogenetic stimulus light and the fluorescence excitation light of the optical fiber photometry system do not affect each other in the fluorescence detection light path through the special fiber customized. The optogenetic stimulation light fluorescence excitation light is modulated to different frequencies,, and then the fluorescence signal of a specific frequency is demodulated to eliminate the influence of optogenetic stimulation light on the optical fiber recording system. Through this system, optogenetic stimulation and multiple fluorescence signals can be recorded simultaneously. Lasers with different wavelengths can be configured to couple the optical path to activate or inhibit experiments on different proteins while recording the fluorescence signal.