Background Congenital heart disease (CHD) is the most common congenital defect in human beings. The purpose of this article is to investigate impact of an integrated management mode of ‘prenatal diagnosis-postnatal treatment’ on birth, surgery, prognosis and complications associated with critical CHD (CCHD) in newborns. Methods A retrospective analysis of the medical records of newborns diagnosed with CCHD were divided into two groups: prenatal diagnosis and postnatal diagnosis. The demographics, clinical characteristics, surgical status, prognosis and complications of the two groups were compared and the differences identified. Results Among the 290 newborns with CCHD, 97 (33.4%) were prenatally diagnosed and 193 (66.6%) were postnatally diagnosed. Newborns in the prenatal diagnostic group were hospitalized immediately after birth, whereas the median age of admission was 6.00 (3.00–12.00) days in postnatal diagnostic group, P=0.000. In terms of postnatal symptoms and signs, the incidence of anhelation, cyanosis and cardiac murmur was higher in the postnatal diagnostic group. The rates of preoperative intubation, postoperative open chest exploration and treatment abandonment were higher in the postnatal diagnostic group. The postnatal diagnostic group was more prone to postoperative complications, such as pneumonia and hypoxic-ischemic brain damage. The preoperative mortality [0 (0.0%) vs. 12 (6.2%), P=0.028] in the prenatal diagnostic group was lower than that in the postnatal diagnostic group. And the one-year survival rate of the prenatal diagnostic group was higher (log-rank test P=0.034). Conclusions The integrated management mode of prenatal diagnosis-postnatal treatment can improve postnatal symptoms, reduces complications, reduces preoperative mortality and increases one-year survival rates in newborns with CCHD.