Congenital birth defects (CBDs) present enormous challenges to global healthcare systems. These conditions severely impact patients' health and underscore issues related to socioeconomic development and healthcare accessibility and efficiency. Previous studies have been geographically limited and lacked comprehensive global analysis. This study provides global, regional, and national disability-adjusted life years (DALYs) data for four major congenital birth defects-congenital heart defects (CHD), neural tube defects (NTDs), digestive congenital anomalies (DCAs), and Down syndrome (DS) from 1990 to 2021, emphasizing health inequalities. The goal is to offer scientific evidence for optimizing resource allocation, focusing on high-burden populations, and reducing disease burden. This study systematically evaluated the global, regional, and national burden of CBDs and their changes from 1990 to 2021 using the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021. To conduct a more focused analysis, four specific CBDs were selected: CHD, NTDs, DCAs, and DS. DALYs were used as the metric, combined with the sociodemographic index (SDI). Analyses included the slope index of inequality and concentration index to measure health inequalities, frontier analysis to estimate achievable outcomes based on development levels, decomposition analysis to identify drivers of disease burden changes, Joinpoint regression analysis to assess temporal trends, and the Bayesian age-period-cohort (BAPC) model to predict future disease burden trends. Compared to 1990, the global burden of the CBDs in 2021 showed a downward trend. Males had a higher burden than females, with the highest burden observed in low-SDI regions. When examining CHD, NTDs, DCAs, and DS specifically, trends in burden changes varied across different CBDs at the global, regional, and national levels. Frontier analysis revealed potential for burden improvement in various countries and territories. Decomposition analysis highlighted differences in disease burden drivers across SDI regions, showing the greatest improvement observed in low-SDI regions. Joinpoint regression analysis indicated a downward trend in DALYs burden across SDI regions, and BAPC model predictions suggested that the burden of CBDs will continue to decline in the future. CBDs pose a major challenge to global public health. Despite an overall decline in disease burden, health inequalities remain prominent, particularly in countries and territories with lower levels of development. Future public health interventions should focus on countries and territories with low levels of development by optimizing healthcare resource allocation, improving basic health infrastructure, enhancing health education, and reducing disease burden inequalities. Global collaboration and data sharing are essential to promote a lifecycle management model for CBDs research and treatment, advancing global health development. This study was supported by the National Natural Science Foundation of China (No. 82270310) and the Jiangsu Provincial Key Research and Development Program (No. BE2023662).