In this prospective cohort study, the effects of a time-lapse monitoring system on embryo quality and clinical pregnancy outcomes were assessed. A total of 608 patients undergoing in vitro fertilization between April 2013 and June 2014 at our institution were recruited for this study and group-matched into a time-lapse monitoring (TLM) (N = 304) or a standard incubator (SI) (N = 304). The patients’ characteristics in the TLM and SI groups were not significantly different. The TLM group showed a significantly higher transferable embryo ratio at Day 3 (61.65% vs. 52.87%; p < 0.0010, RR =1.10 [1.02, 1.19]), a higher number of transferable embryos (4.71 ± 2.38 vs. 4.09 ± 2.35; p = 0.0053, SMD =0.26 [0.06, 0.46]) and number of good-quality embryos cryopreserved at Day 3 (2.72 ± 2.35 vs. 2.11 ± 2.33; p = 0.0056, SMD =0.26 [0.06, 0.46]). In addition, the implantation and clinical pregnancy rates were not statistically significant between the TLM and SI groups. However, the TLM group had a higher ongoing pregnancy rate (67.32% vs. 57.22%; p = 0.0410) and live birth rate (65.37% vs. 55%; p = 0.0380) compared with the SI group. The observed beneficial effects could be the result of a more stable environment provided by the TLM system.