Objective：To investigate whether alternative splicing regulate the stage transition of follicle assembly in mice，the transcriptome data of single germ cells in new born mouse ovary were analyzed. Methods：Bioinformatics analysis were performed on transcriptome data of single germ cells in mice to detect alternative splicing events in three cell development stages during follicle assembly and differential alternative splicing events between stage transitions. PCR was used to validate dynamic stage transition related isoform expression. Results：The current study found abundant differential alternative splicing events between stage transitions during follicle assembly in mice. The most enriched splicing events were detected in follicle stage，also the most enriched differential splicing events were detected between cyst break down and follicle stage. The results of PCR validated the presence of isoforms of meiosis related genes and showed their shifts of alternative isoform usage at stage transitions. Conclusion：Alternative splicing was associated with cell development stage transitions during follicle formation in mice，regulating the transformation from germ cell to oocytes.