The advancement of intelligent navigation will lead the shipping industry and a profound change in our country’s navigation higher education. Based on the analysis of the current problems faced by China’s navigation education and the demand for intelligent navigation, this paper puts forward the general ideas and strategies for the reform of the training mechanism of compound intelligent navigation talents based on the integration of navigation technology, Marine engineering and multi-disciplines, and explores the training path of compound intelligent navigation talents, which can be used for reference for the training of “Emerging Engineering Education” talents in navigation in China’s higher education.