The invention provides a microsatellite unstable site screening and analysis model construction method and device. The method comprises the following steps of: S1, taking a microsatellite site of a reference genome as a candidate MS site, S2, selecting a plurality of samples with known microsatellite instability detection state information as training set samples, carrying out mutation detection on candidate MS site areas of the training set samples, respectively recording mutation types and numbers, and calculating information entropy of mutation of each candidate MS site, and S3, correlatingthe microsatellite instability detection state information with the entropy of the information entropy of the mutation of each candidate MS site, selecting an entropy threshold of each candidate MS site for distinguishing the microsatellite instability detection result, and screening out the candidate MS site with a high distinguishing degree as an MSI site. According to the scheme, the problemsof low detection efficiency caused by excessive fixed MSI sites and low detection specificity and sensitivity caused by incapability of covering all types of samples in the prior art are solved.