Human embryonic stem cells (hESCs) hold great promise for future clinical cell therapies because of their unique potential to differentiate into all human cell types. However, the destruction of normal fertilized embryos and the derivation of hESCs for research has resulted in polarized ethical debates, with most of the controversy centered on embryo destruction. Therefore, due to less ethical controversy surrounding them, abnormal fertilized zygotes that are usually discarded are a potential feasible resource for the derivation of hESCs. Microsurgery on human polyspermic zygotes can contribute to the derivation of hESCs, but the efficiency is much lower. Here, we reported a culture system to enhance the developmental competence of such microsurgical human polyspermic zygotes by EGF-BDNF-IGF-1 combination, which eventually resulted in the increased derivation efficiency of hESCs from them. We found that the developmental efficiency of microsurgical enucleated tripronuclear (3PN) embryos cultured with the EGF-BDNF-IGF-1 combination was significantly increased compared with the control group. More importantly, when the microsurgical enucleated 3PN embryos were cultured in medium supplemented with EGF-BDNF-IGF-1, the frequency ratio of chromosome abnormality was reduced. Our present study will facilitate the development of hESC line derivation in subsequent studies and also provide an additional choice for infertile couples.