The invention discloses a genetic diversity analysis method for a inbreeding male giant freshwater prawn, which comprises the following steps of: step 1, acquiring inbreeding giant freshwater prawn samples with different traits, and extracting the DNA; step 2, selecting a microsatellite marker combination and designing a specific PCR primer set for amplification; step 3, evaluating the number of PCR products and observing the genotype and size of the alleles; step 4, recording the allele number A, the allele duplication number G, the observed heterozygosity Ho, the desired heterozygosity He, and the accuracy deviation value P based on the Hardy-Weinberg equilibrium law of each prawn, and analyzing the difference of the microsatellite sites; calculating the gene flow Nm according to the frequency parameters of the population allele; gene spacing is determined by using the gene Nei coefficient method. According to the invention, based on the microsatellite analysis method, the method provides a genetic diversity analysis method for a inbreeding male giant freshwater prawn, which is very suitable for researching the genetic structure of different near-parent male prawn groups, and provides a high-quality male parent for the giant freshwater prawns.