The invention relates to a microfluidic detection system for non-tuberculosis mycobacterium strain identification, the detection system uses a microfluidic chip for detection, the microfluidic chip comprises a chip body, the chip body is provided with a sample adding hole, a main flow channel, a micro flow channel and a reaction hole; the reaction holes comprise a positive quality control hole, a positive control hole and at least one detection hole; the sample adding hole is communicated with the main runner; each reaction hole is communicated with the main flow channel through the micro flow channel; and each detection hole contains a specific detection primer group of the nontuberculous mycobacterium. Through the microfluidic monitoring system, more than ten nontuberculous mycobacteria strains can be simultaneously subjected to specific detection under isothermal conditions, and the microfluidic monitoring system has the advantages of good specificity, high sensitivity, simplicity in operation, rapidness in detection and the like, and has a good clinical application prospect.