Nonprofit foundations are becoming increasingly significant stakeholders in global governance and business operations. However, measuring their efficiency is a challenging task due to their mission-driven nature. This study aims to investigate the factors influencing the program efficiency of nonprofit foundations in China. 10 indicators are employed and tested using data from the Chinese Research Data Services (CNRDS) platform. The study employs multiple regression analysis to examine the influential factors identified in the dataset. The study's findings suggest a positive and significant correlation between registration level and program efficiency, while there is a negative and significant correlation with administrative efficiency. Furthermore, organizational income appears to moderate the impact of registration level on both program and administrative efficiency. The results of the analysis provide valuable insights for nonprofit foundation operators, policymakers, and researchers in the field of the nonprofit sector (e.g., nonprofit foundations in China are encouraged to find an equilibrium between their organizational efficiency and their registration status). In terms of theoretical contributions, this study stands as one of the pioneering efforts in investigating the influence of registration levels and the moderating effect of organizational income on nonprofit foundations’ efficiency. Finally, we have delineated its limitations and outlined avenues for future research.