The invention discloses a method for efficiently separating mouse spermatogonial stem cells. The method includes the following steps that firstly, mouse testis are collected, and a testicular cell suspension is prepared through a two-step enzyme digestion method; secondly, the testicular cell suspension is inoculated in a porous plate according to a certain density, and a spermatogonial stem cell culture solution is added for in-vitro culture; thirdly, the culture solution is removed, testis cells of different times are cultured through tryptic digestion, and spermatogonial stem cells are sorted from the testis cells through the magnetic activated cell sorting; fourthly, the sorted spermatogonial stem cells are inoculated to an STO trophoblast, and a spermatogonial stem cell culture solution is added for primary culture and subculture of the spermatogonial stem cells. A mouse spermatogonial stem cell system is built through the method including the steps of separation, culture, re-separation and re-culture. The method can achieve the aim of efficiently enriching the spermatogonial stem cells in vitro, and is economical and easy to implement, so that a direction is provided for protection of rare animal varieties and treatment of male infertility.