Fuel cells are made from fuel and oxygen. Because of its low pollution, high energy conversion efficiency and high reliability, fuel cell has become the future direction of new energy application, the technological development path in the field of fuel cell research has great significance to the development of technological and energy innovation. Using the patent analysis method, this paper analyses the patent data from Derwent Innovation Index quantitively to study the state of application for patents, core technologies, highly cited patents and the main patentees. It shows that auxiliary device and related methods were a research hotspot in recent years; as the biggest patent holder of fuel cell technologies, Toyota, Honda motor Co. and Nissan motor Co. have an advantage. This paper has discovered some potential problems behind the phenomena and some suggestions are put forward finally.