Although ventricular septal defect (VSD) is a common and simple congenital heart disease in newborns, its true incidence and spontaneous closure (SC) rate remains topics of controversy. This study aims to provide data on the true incidence and SC rate of VSD in the Chinese neonatal population. We conducted a prospective study at 3 hospitals, all newborns underwent echocardiography. Those with a diagnosis of isolated VSD were included in the study group and underwent a 7-year follow-up period. In 6,750 newborns, VSDs were detected in 113 cases (incidence rate of 16.7%), accounting for 62.8% of congenital heart disease, of which 35 were perimembranous (5.2%), 72 were muscular (10.7%), and 6 were doubly committed juxta-arterial (0.9‰). During the 7-year follow-up period, 18 cases required surgical or transcatheter closure. The SC rate in those with perimembranous VSD and muscular VSD (mVSD) were 51.4% (18 of 35) and 97.2% (70 of 72), respectively. Excluding doubly committed juxta-arterial, perimembranous site and defects ≥4 mm are risk factors for VSD that do not spontaneously close. Independent predictive factors for perimembranous VSD which do not spontaneously close is defects ≥4 mm. There was no significant difference in the SC rate at different times between the 4 mVSD sites. In conclusion, this study provides the true incidence and SC rate for Chinese newborns with VSD.