BackgroundCongenital heart disease (CHD) is the leading cause of mortality in childhood worldwide. However, a large number of children with CHD are not diagnosed promptly in low- and middle-income regions, due to limited healthcare resources and lack the ability of prenatal and postnatal ultrasound examinations. The research on asymptomatic CHD in the community is still blank, resulting in a large number of children with asymptomatic CHD can not be found and treated in time. Through the China-Cambodia collaborative health care initiative, the project team conducted research, screened children’s CHD through a sampling survey in China and Cambodia, collected relevant data, and retrospectively analyzed the data of all eligible patients.ObjectivesThe project aimed to evaluate the prevalence of asymptomatic CHD in a sample population of 3-18years old and effects on their growth status and treatment outcomes.MethodsWe examined the prevalence of ‘asymptomatic CHD’ among 3-18years old children and adolescents at the township/county levels in the two participating. A total of eight provinces in China and five provinces in Cambodia were analyzed from 2017 to 2020. During 1 year follow-up after treatment, the differences in heights and weights of the treated and control groups were evaluated.ResultsAmong the 3,068,075 participants screened from 2017 to 2020, 3967 patients with asymptomatic CHD requiring treatment were identified [0.130%, 95% confidence interval (CI) 0.126 -0.134%]. The prevalence rate of CHD ranged from 0.02 to 0.88%, and was negatively related to local per capita GDP (p = 0.028). The average height of 3310 treated CHD patients were 2.23% (95% CI: -2.51%~-1.9%) lower than that of the standard group and the average weight was − 6.41% (95% CI: -7.17%~-5.65%) lower, the developmental gap widening with advancing age. One year after treatment, the relative height difference remained comparable while that, in weight was reduced by 5.68% (95% CI: 4.27% ~7.09%).ConclusionsAsymptomatic CHD now is often overlooked and is an emerging public health challenge. Early detection and treatment are essential to lower the potential burden of heart diseases in children and adolescents.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12872-023-03314-8.