The aim of this study was to explore whether the morphology of polar bodies (PBs) estimated at 16–18 h after insemination can be used as an additional marker for predicting human embryo quality or pregnancy outcome. The data from 355 patients who received standard in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) treatment after controlled ovarian hyperstimulation were recruited. Normal fertilized 3048 zygotes from 382 cycles were divided into two groups, PBs intact or fragmented, according to the morphology of PBs assessed at 16–18 h after insemination. Embryo quality and pregnancy outcome were compared between the two groups. It was shown that the day 3 (D3) good embryo rate, good quality blastocyst rate and available embryo rate of the PBs intact group were all significantly higher than that of the corresponding fragmented groups. However, no significant differences in pregnancy rate (PR) or implantation rate (IR) were observed between the intact and fragmented groups. Although PBs morphology estimated at 16–18 h after insemination had little effect on PR or IR in fresh embryo transfer cycles, a better embryo quality can be achieved in the PB-intact group, which is valuable for embryo selection.