Newborn Screening Programme for Congenital Heart Disease (CHD) in Shanghai has been in operation for over 5 years, and its feasibility and effectiveness still lack a systematic and comprehensive evaluation. This study aimed to detail the implementation of the programme and evaluate its results, benefits, and reliability in clinical practice. This study was an observational study involving all newborns received CHD screening in Shanghai from 2017 to 2021. Pulse oximetry (POX) plus cardiac murmur auscultation (namely the dual-index method) was used for CHD screening in newborns aged 6-72h. Newborns who screened positive was recommended for echocardiography, and those diagnosed with CHD would be planned for further evaluation and intervention. Data were aggregated by birth year and district of birth. Results of neonatal CHD screening, diagnosis and treatment, and temporal trends of infant mortality rate (IMR) and the proportion of under-five mortality (U5M) attributed to CHD were analysed. A retrospective cohort study was also conducted to assess the reliability of the dual-index method in clinical practice. In total, 801,831 (99.48%) newborns were screened for CHD, 16,489 (2.06%) were screened positive, and 3541 (21.47%) of the screened-positive newborns were identified with CHD. Seven hundred and fifty-two patients with CHD received surgical or interventional treatment with a successful rate of 94.81%. The period from 2015 to 2021 witnessed an approximately twofold decrease in IMR from 4.58‰ to 2.30‰, and a downtrend in the proportion of U5M attributed to CHD from 25.93% to 16.61%. High sensitivity and specificity of the dual-index method in clinical practice were observed for both critical (100.00% and 97.72%) and major CHD (98.47% and 97.76%). Newborn screening programme for CHD has been well implemented in Shanghai, and this programme is a successful public health intervention to reduce infant death. Our study provides encouraging evidence and experience for implementing newborn screening programme for CHD nationwide in China. This study was supported by the National Key Research and Development Programme of China (2021YFC2701004 and 2016YFC1000506), CAMS Innovation Fund for Medical Sciences (2019-I2M-5-002), and Three-Year Planning for Strengthening the Construction of Public Health System in Shanghai (No. GWIV-24).