The construction of satellite navigation is characterized by a long risk chain, multiple related industries, various participants, multiple interests, and difference in domestic and foreign characteristics; therefore, its governance is strongly systematic and highly complex. In the context of promoting the modernization of China’s national governance system and capacities, the satellite navigation industry needs to actively explore a modernized governance system and development mode to improve its governance quality and efficiency and ensure its sustainable development. Considering multiple levels such as history vs. reality and theory vs. practice, this study summarizes the governance experience in the practice of the three-step development strategy of China’s satellite navigation system and analyzes the major challenges it faces in the new development stage. Moreover, the development goals and the factors to be coordinated for the modernized governance are proposed. Furthermore, we suggest that efforts should be focused on improving the leadership, management, legal, application, innovation, strategic talent cultivating, and internationalization systems. This can promote the modernized governance of satellite navigation construction and provide strong support for the high-quality development of China’s satellite navigation system.