Objective To explore variations of expressions of a group of miRNAs that highly express in spermatogonial stem cells (SSCs) during different stages of testis development and the regulation of proliferation and apoptosis of SSCs cultured in vitro by miR-125a. Methods The variations of expressions of 34 miRNAs during different stages of testis development were explored by the real-time RT-PCR. SSCs cultured in vitro were infected with lentivirus particles with over-expression and expression suppression of miR-125. The effects of miR-125a on the proliferation and apoptosis of SSCs cultured in vitro were explored by CCK8 assay, EdU incorporation, and double staining of Hoachst 33342 and propidium iodide (PI). Finally, real-time RT-PCR and Western blotting were adopted to verify whether the proapoptotic gene Bak1 was the target gene of miR-125a. Results Different miRNAs had different expression patterns during the testis development. MiR-125a increased the number of SSCs cultured in vitro and decreased the apoptosis. Over-expression of miR-125a decreased mRNA and protein expressions of Bak1 in SSCs cultured in vitro, while expression suppression of miR-125a increased mRNA and protein expressions of Bak1 in SSCs cultured in vitro. Conclusion Different miRNAs have different expression patterns during the testis development. MiR-125a can regulate the apoptosis and proliferation of SSCs and Bak1 is a target gene of miR-125a in SSCs.