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 witha 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.