The invention relates to the technical field of microsatellite site detection, in particular to a method and system for detecting the instability state of a microsatellite; and the method comprises the following steps: carrying out DNA extraction, fragmentation treatment, terminal repair and joint connection on a cancerous tissue sample; carrying out amplification, hybridization, capture, PCR amplification and purification to obtain a sequencing library; and obtaining targeted capture sequencing data of a tumor tissue sample through second-generation computer sequencing, and carrying out information analysis related to microsatellite instability state detection according to an MSI model. Compared with the prior art, the genetic information of the tumor tissue of the testee is obtained by adopting the current mature next-generation sequencing technology, single tumor tissue analysis can be carried out, dependence on a control sample is avoided, the limitation of microsatellite detectionis broken through, the method can be suitable for multiple gene combinations, an MSI site probe does not need to be specially designed, and the applicability is high; moreover, the detection cost canbe saved, the method is efficient, systematic, economic, simple and convenient, and the detection sensitivity is improved.