Objective To analyze the incidence and influencing factors of preterm birth (PTB), low birth weight (LBW) and small for gestational age (SGA) neonates with congenital heart disease (CHD) in Changsha City, to provide a scientific basis for the development of target preventive measures. Methods Neonates with CHD reported by all obstetrics institutions in Changsha City from 2022 to 2023, elucidating the incidence of PTB, LBW and SGA. Statistical methods such as Chi-square tests and binary logistic regression were utilized to determine the associations of influencing factors with PTB, LBW and SGA neonates with CHD. Results A total of 1040 neonates with CHD were eligible for analysis, and the incidence of PTB, LBW and SGA were 15.00% (156/1040), 13.27% (138/1040) and 12.12% (126/1040), respectively. Binary logistic regression analysis showed that both taking folic acid during pregnancy (aOR = 0.386, 95% CI: 0.217–0.687), and parity 1 (aOR = 0.400, 95% CI: 0.243–0.659) or 2 (aOR = 0.278, 95% CI: 0.160–0.482) were protective factors for PTB While cesarean delivery (aOR = 2.517, 95% CI: 1.725–3.671) was a risk factor for PTB. Cesarean delivery (aOR = 2.130, 95% CI: 1.447–3.134), female infants (aOR = 1.589, 95% CI: 1.100–2.297), midwifery institutions of municipal level or above (aOR = 2.379, 95% CI: 1.334–4.245) were risk factors for LBW. Parity 1 (aOR = 5.083, 95% CI: 1.824–14.164) was a risk factor for SGA, while assisted reproduction(aOR = 0.332, 95% CI: 0.131–0.838) was a protective factor. Conclusions The incidence of PTB, LBW and SGA neonates with CHD in Changsha City is not in high level, and it was affected by maternal folic acid consumption, parity, mode of delivery, level of midwifery institutions, mode of conception, as well as neonatal gender.