Objective The purpose of this study is to conduct an economic cost-effectiveness analysis of newborn screening with congenital adrenocortical hyperplasia(CAH)and glucose-6-phosphate dehydrogenase(G6PD)deficiency to provide evidence-based decisions for health departments.Methods This study selected the provinces which had carried out CAH and G6PD deficiency screening to understand the current situation and morbidity.According to the relevant literature and social research results to conduct a cost-effectiveness analysis.Results The nationwide CAH screening has good cost-benefit of input and output ratio above 1∶2.4.However,when the incidence of G6PD deficiency is above 1∶2781,the output is higher than the input.Conversely,the input is higher than output.Conclusion Neonatal screening for CAH and G6PD deficiency can bring significant economic and social benefits.