The purpose of this study was to evaluate whether the blastocyst morphologic grading and the protocol of controlled ovarian stimulation (COS) would influence pregnancy outcomes, aiming to provide guidance when choosing blastocyst transfer. The clinical data of 612 patients who received single fresh blastocyst transfer for first cycle, as well as the data of 253 patients who had already delivered were analyzed retrospectively. The patients were divided into two groups according to blastocyst formation time (D5 or D6). The following subgroup analyses were performed: (i) the morphologic grading of blastocyst and (ii) the protocol of COS. We observed that D5 single embryo transfer (SET) were associated with higher clinical pregnancy rate (CPR, 59.04% vs. 31.73%, P < 0.001) and live birth rate (LBR, 43.90% vs. 24.04%, P < 0.001) than D6 SET following fresh cycle. Patients in D5 group experienced more good blastocysts transfer (45.47%vs. 13.46%, P < 0.001) and less poor blastocysts transfer (9.64%vs. 45.19%, P < 0.001) than patients in D6 group. As to early stage and good quality blastocysts, the CPR and LBR were similar between D5 and D6 group. GnRH antagonist protocol had a demonstrable inferiority comparing with the early-follicular-phase long-acting GnRH-agonist long protocol (EFLL) or the mid-luteal-phase long-acting GnRH-agonist long protocol (MLLL) with regard to the CPR and LBR in D6-SET group. The analysis found that ovarian reserve of patients in D6-SET group was comparatively worse than that of patients in D5-SET group and D6-SET patients represented a subgroup of infertility patients usually having relatively poor embryo quality. The results should be interpreted with caution as the very low numbers in the respective group limited the use of statistical tests and the real significance values.