Objective To analyze and evaluate the population genetic quality of 3 subbreed China agricultural university miniature pigs in Beijing. Method According to the local standard DB11/T828.3-2011, 25 pairs of microsatellite primers were used in 3 subbreed China agricultural university miniature pigs. And software Popgen32 was used to process the data. Results 24 microsatellite loci shared 130,122 and 138 alleles in China agricultural university miniature pig Ⅰ, Ⅱ, III respectively. The average heterozygosity was 0.6759,0.5967 and 0.6779 respectively, while the average polymorphism information content (PIC) was 0.6344、0.5540 and 0.6403 respectively. The genetic distance between China agricultural university miniature pig Ⅱ and III was 0.4251, while the genetic distance between China agricultural university miniature pig Ⅰ and Ⅱ was 0.2084. Conclusion In 3 subbreeds, China agricultural university miniature pig Ⅱ and III have genetic stability and genetic diversity，and both of which satisfied with the genetic characteristics of closed colony laboratory animal．