An embodiment of the invention discloses a multi-channel fluorescence detection system which comprises n excitation light sources, n light beam adjusting units, a convergent mirror, a light splitting unit and n fluorescence detection units. The n excitation light sources are used for transmitting light beams in different wave bands; each light beam adjusting unit corresponds to the single corresponding excitation light source and is used for adjusting the collimation and the directions of the light beams emitted by the excitation light source; the first convergent mirror is arranged between the light beam adjusting units and a to-be-detected sample and is used for converging emergent light beams from the light beam adjusting units onto the to-be-detected sample, so that fluorescence can be generated by means of excitation, and fluorescence generated by the to-be-detected sample can be collimated; the light splitting unit is used for receiving fluorescence collimated by the first convergent mirror, splitting the fluorescence to obtain fluorescence excited by the light beams transmitted by the various excitation light sources and projecting the fluorescence to the corresponding fluorescence detection units; each fluorescence detection unit corresponds to the single corresponding excitation light source and is used for detecting the fluorescence. The multi-channel fluorescence detection system in the embodiment of the invention has the advantage that the accuracy of detection results and the detection efficiency can be improved.