The present invention provides a multi-channel fluorescence detecting system for detecting a plurality of fluorescence labeled analytes. The multi-channel fluorescence detecting system comprises a light source, a light filter device, a dual branch light guide tube, and a detector. The light source comprises a plurality of sub light sources for respectively providing an excitation light. The plurality of sub light sources are a plurality of single color Light emitting diodes (LEDs) which can be selectively turned on or off. The light source generates a plurality of lights with full width at half maximum (FWHM) wavelengths formed in a non-overlap manner. With the disposition of the plurality of sub light sources, the accuracy for detecting the specific analytes is raised, the light flux with a specific wavelength band is effectively raised (without raising the light flux of the full wavelength band), the structure is simplified, and the manufacturing cost is decreased.