The invention relates to a micro-fluidic chip-based gene detection system and a detection method thereof. The detection system comprises a shell, a micro-fluidic chip, an optical device and a rotatingdevice. The micro-fluidic chip is arranged in an accommodating cavity, the micro-fluidic chip is provided with sample adding cells, sample separating elements and reaction elements, and every reaction element comprises a plurality of reaction cells loaded with various detection agents. The detection system has the advantages of realization of simultaneous detection of various pathogenic microorganisms through one-time sample loading, simple sample treatment steps, high detection efficiency, easiness in control of the sample adding volume, realization of the volumes of samples-to-be-detected entering all the reaction cells being same to each other, accurate detection result and automatic detection process, and meets the application requirements of high-efficiency and rapid detection and checking of a lot of pathogenic microorganisms in the port health quarantine.