Although assisted reproductive technology (ART) has been developed in many mammalian species including cows, the only embryo preservation technology that is available is cryopreservation. In the present study, small molecules were used to preserve embryos at room temperature. The basic medium for embryo preservation consisted of 1% BSA non-cryopreservation medium (BNC) instead of fetal bovine serum (FBS). To maintain survival and prevent damage during embryo storage, three candidate small molecules were selected—CHIR99021, Y-27632 and Thiazovivin—and their concentrations were optimized. Then, the embryos in the small molecule supplemented preservation medium were stored at room temperature. The viability and hatching rate of embryos stored at 10°C were greater for Y-27632-BNC and CHIR99021+Y-27632-BNC compared to BNC. However, the rate was lower for Thiazovivin-BNC compared to BNC. Although there were no surviving embryos after storage at 20°C, the viability and hatching rate of embryos significantly increased in Y-27632-BNC and CHIR99021+Y-27632-BNC compared to BNC. The mechanism by which small molecules enhance survival of embryos during storage was investigated, and expression of heat shock protein 70 was observed to increase. The findings of this work may be useful in improving ART in the agricultural field.