Background The number of D3 embryo blastomeres affects pregnancy outcomes in patients undergoing cleavage-stage embryo transfer. However, the association between blastomere number in D3 embryos and pregnancy outcomes after vitrified–thawed single blastocyst transfer remains unknown.Methods This retrospective cohort follow-up study included 2,274 cases of vitrified–thawed single blastocyst transfer,all patients were divided into six groups according to blastomere number of D3 embryos: ≤5, 6, 7, 8, 9, and ≥ 10 cells. The primary outcome was the live birth rate (LBR). The secondary outcomes were the clinical pregnancy rate, miscarriage rate, and neonatal outcomes. Statistical analyses were performed using a multivariate logistic regression model to explore the association between blastomere number in D3 embryos and LBR.Results The LBR significantly increased with the number of blastomeres in D3 embryos (28.4%, 36.4%, 42.5%, 46.1%, 45.2%, and 58.1%; p < 0.001). Furthermore, the results of the high- and low-quality blastocyst subgroup analyses showed significant differences in the LBR among the groups (p < 0.01). As the number of blastomeres in D3 embryos increased, the miscarriage rate significantly decreased (23.3%, 18.6%, 14.0%, 15.9%, 13.6%, and 8.9%; p < 0.05). However, the number of blastomeres did not affect perinatal outcomes. Multivariate logistic regression analysis after adjusting for confounding factors revealed significantly decreased LBR in the ≤ 5-cell group (adjusted odds ratio [aOR]: 0.627, 95% confidence interval [CI]: 0.442–0.891; p < 0.01) and significantly increased LBR in the ≥ 10-cell group (aOR: 1.612, 95% CI: 1.230–2.112; p < 0.01) compared with that in the 8-cell group.Conclusions The number of blastomeres in D3 embryos may be an important factor in selecting blastocysts during vitrified–thawed single blastocyst transfer cycles. The transfer of a single blastocyst arising from ≥ 10-blastomere D3 embryo may reduce the miscarriage rate and improve LBR.