There are three systems and applications of fuel cells in China, namely transportation fuel cells, stationary systems and portable fuel cells. It is important for China to analyze the supply and the cost of fuel cells in the context of the energy crisis. After introducing the current situation of three systems, this article classified the existing policies, and made some analysis of the policy effects. Then a PEST–SWOT model was employed to summarize the strengths and weaknesses for fuel cells. Considering the own features of the three applications, different development strategies were put forward. Based on the above strategies, some conclusions were drawn about the development direction and framework of whole fuel cell systems in China. Finally, we proposed some prospects and suggestions on the fuel cell systems.