FKBP12, known as FK506 binding protein, binds to immunosuppressive drug FK506, which must be taken by patients who received organ transplant. The side effect of FK506 is that women have difficulties in bearing a baby, so it is important to find the reason of their subfertility. This research explored the expression of FKBP12 in pre-implantation embryos and investigated its potential effect on reproduction. The results demonstrate that FKBP12 had good co-localization with endoplasmic reticulum and inositol-1, 4, 5- trisphosphate receptor in pre-implantation stages. Inhibiting FKBP12 by FK506 significantly increased the rate of 1-cell and fragmented embryos, greatly reduced the rate of 2-cell embryos during in vitro fertilization. When the mice received FK506 by gavage for 21 days, the calcium intensity of oocytes was decreased, these mice were subfertile and gave birth to significantly less pups during 6-month breeding period. QPCR demonstrated that Fbxo43 and P27kip, which are related to the release of MII oocyte arrest, and calcium channel partner protein Orai1 were downregulated, while Cdc2 and Ca2+ sensor at ER, stromal interaction molecule 1 (Stim1) were upregulated for a short time after adding FK506. Further exploration discovered that FK506 treatment increased Ca2+ concentration in the cytoplasm and caused pronucleus formation, however, the rate of parthenogenetic activation was lower compared to SrCl2 group. These findings identify the previously unknown role of FKBP12 in female reproduction which contributes to the release of calcium via IP3 R channel and might open up new strategies for women who want to bear a baby after transplantation.