To promote the construction of high-quality “Golden Course” for fuel cell courses and solve the educational pain points including insufficient advancedness and systematicity in curriculum teaching, so as to meet the training demands of interdisciplinary engineering talents in the field of new comprehensive energy, this paper sorts out and analyzes the core problems existing in current fuel cell teaching in colleges and universities. At present, fuel cell courses are faced with prominent fragmentation of knowledge systems. Most teaching adopts modular and scattered lecture modes with disjoint multidisciplinary knowledge points and disconnection of knowledge before and after the curriculum. As a result, students cannot build a complete and systematic knowledge framework covering basic principles, core components, stack integration, and engineering applications, and their ability to integrate and transfer knowledge is weak. Meanwhile, traditional teaching only focuses on fuel cells as a single power generation device and a single energy conversion dimension, ignoring the industrial application characteristics of multi-energy coupling conversion among hydrogen energy, electric energy, and thermal energy as well as the coordinated operation of wind-solar-hydrogen-energy storage systems. Teaching fails to cultivate students’ systematic thinking of multi-energy coupling, leading to the common lack of overall engineering vision and system optimization thinking among students, and making it difficult for them to tackle complex engineering problems of comprehensive energy systems. The above problems disconnect curriculum teaching from actual industrial demands and restrict the improvement of education quality and connotation construction of golden courses. By clarifying the existing defects of fragmented teaching and lack of systematic vision, this paper provides a problem basis and reform reference for reconstructing systematic, coupled, and cutting-edge curriculum knowledge systems, optimizing advanced teaching modes, and building high-quality fuel cell golden courses for cultivating interdisciplinary new energy talents.