Objective To investigate the effect of Salvia miltiorrhiza on the morphological structure and ultrastructure of mouse ovarian tissues frozen and thawed at the early developmental stage after transplantation. Methods The 1- day ovaries-thawed through cryopreservation treatment were xenografted into the donated kidney capsule of 8 to 12-week-male mice. The mice in two groups were sacrificed at day 2, 7 and 14 after transplantation respectively, and the ovaries transplanted were excised for observing histological structure and ultrastructure changes and for counting the ovarian follicles and detecting the apoptosis index of follicles. Results The survival rate of primordial follicles in the mouse ovaries-frozen and thawed was 87.9%. The histological structure and ultrastructure showed that both the follicles and stromata were damaged on day 7 after transplantation. The follicular structure had been recovered for 14 days. The number of follicles and survival rate after transplantation in Salvia miltiorrhiza group (30.1%) were higher than that in saline group(13.2%) at 14-day(EM>P/EM><0.05). Conclusion The injury of the mouse ovarian tissues at the early stage is due to the ischemia and hypoxia rather than the cryopreservation. Salvia miltiorrhiza may provide benefits for folliculogensis and decrease the apoptosis index of follicles.