With the changes of social and economic development, more and more people pay attention to the development of non-profit organizations, and the performance research of non-profit organizations has become the focus of research. As the internal governance organization of non-profit organization, the board of directors and the management organization are related internal factors that will affect the organizational performance of non-profit organization. Based on the data of Form 990 of the US Internal Revenue Service, this paper conducted an empirical study on the relationship between internal governance and organizational performance of non-profit organizations, and studied the moderating effects of board size, average weekly working hours, number of managers, members’ work involvement and compensation incentives on internal governance and organizational performance of non-profit organizations. The results show that the number of managers in non-profit organizations is negatively correlated with organizational performance, the average weekly working hours of managers are significantly correlated with organizational performance, and the compensation of managers is significantly correlated with organizational performance. Through the empirical demonstration, this study promotes the management and development practice of non-profit organizations, and lays a solid foundation for the construction of socialist harmonious society in China.