The invention discloses a new comprehensive-deafness related-gene mutation detection system. According to 6 known genes related to a Waardenburg syndrome at present, the deafness-gene mutation detection system is composed of 59 selected detection loca, target areas are hybridized and connected through the high specificity of a ligation reaction of ligase, and then different-length ligation products corresponding to the loca are obtained in the mode that non-specific sequences with the different lengths are led into the end sections of ligation probes, and the ligation reaction of ligase is carried out, and the ligation products are subjected to PCR amplification through universal primers for marker fluorescence. The new comprehensive-deafness related-gene mutation detection system has the advantages that an existing multiple-nucleic-acid-molecule amplification technology is improved, the specific detecting probes are designed, specific ingredients of the detecting system and the specific reaction conditions are set, rapid copy-number-variation detection is carried out through the 59 loca on the 6 known genes related to the Waardenburg syndrome, detection can be completed within one working day, and the accurate detecting result can be obtained through lowest 200 nanograms of DNA.