Objective To explore whether thin endometrial thickness (EMT) is associated with singleton low birth weight (LBW) from single fresh blastocyst transfer. Design Retrospective cohort study. Setting Reproductive center. Population All women were ≤40 years old and underwent single fresh blastocyst transfer and singleton live birth. Interventions None. Methods Multivariable logistic regression was used to evaluate the association between thin EMT and singleton LBW. Main outcome measures LBW was the primary concern of this study. Results In total, 2847 women met the study inclusion criteria. The neonatal birthweight in the EMT ≤7.5 mm group was significantly lower than that in the EMT 7.6~12.0 mm and EMT >12.0 mm group (P<0.001). The rate of LBW in the EMT ≤7.5 mm group was 24.9%, which was significantly higher than the 4.0% in the EMT 7.6~12.0 mm group and the 5.3% in the EMT >12.0 mm group (P<0.001). The total neonatal malformation rate was similar between the groups (1.1%, 0.8% and 1.5%, P=0.21). After multiple logistic regression analysis, EMT≤7.5 mm was an independent risk factor for LBW (adjusted odds ratio [AOR]: 4.39, 95% CI: 1.85～10.46, P<0.001). Conclusions Thin EMT (≤7.5 mm) on the hCG trigger day is an independent risk factor for singleton LBW from single fresh blastocyst transfer. The neonatal birthweight in the EMT ≤7.5 mm group was significantly lower than that in the EMT 7.6~12.0 mm and EMT >12.0 mm groups. The total neonatal malformation rate was comparable between the groups.