Fuel cell technology and its industrialization have been developed rapidly in China in recent years. However, the high cost of the fuel cell caused mainly by the using of precious Pt catalysts is still one of the most important factors restricting the development of fuel cell commercialization. It is of great significance to develop low Pt catalysts with much higher catalytic efficiency and lower Pt loadings. In recent years, Pt-based catalysts with three-dimensional morphology or nanostructure have been emerged as a type of ultra-important low Pt catalysts, due to their special morphologies/structures, their catalytic activity are usually much higher than that of the widely used Pt/C catalysts. In this paper, the research progress of Pt-based catalysts with special three-dimensional morphology (such as nanoframe structure, flower-like structure, nanocage structure, sea urchin structure, etc.) and their applications in fuel cells are reviewed, meanwhile, some weaknesses and challenges of these catalysts are concluded; Furthermore, the future development and application of these catalysts are prospected.