The invention discloses a microsatellite primer for macrobrachium nipponensis diversity analysis. The microsatellite primer for macrobrachium nipponensis diversity analysis comprises eleven pairs of microsatellite primers, which are respectively MN01, MN02, MN03, MN04, MN05, MN06, MN07, MN08, MN09, MN10 and MN11; meanwhile, the invention also provides application of the microsatellite primer in macrobrachium nipponensis population genetic structure analysis through a following method comprising the steps: (a) extracting genome DNA (Deoxyribose Nucleic Acid) to be analyzed; (b) adopting the genome DNA as a template, and adopting the microsatellite primer for carrying out PCR (Polymerase Chain Reaction) molecular marker detection; (c) carrying out genetic structure analysis. The microsatellite primer provided by the invention has the characteristics of stable PCR amplification results, high polymorphism and the like, can be used to utilize molecular markers for carrying out genetic diversity analysis, population genetic structure analysis, genetic map construction, gene mapping, variety identification, germplasm preservation, quantitative trait gene analysis, evolution and phylogenetic relationship research and the like, and has a better application value.