Fuel cells are emerging as promising power sources and have attracted increasing attention from industries and academics worldwide. In particular, automotive manufacturers are replacing internal combustion engines in vehicles with fuel cell systems, which are advantaged by zero emissions, high efficiency, and various clean routes that generate pure hydrogen. However, current fuel cell systems are costly, and their corresponding infrastructures are not fully qualified to meet current market demand. This paper reviews the challenges and developments of automotive fuel cell hybrid power systems and their controls. It briefly summarizes the model, control, and optimization issue associated with the research and application of fuel cells in hybrid power systems. After presenting the basic knowledge and discussing the trending size and structure of fuel cells for automotive usage, the review describes models of automotive fuel cell systems, focusing on the electrochemical reaction dynamics and the key parameters influencing their efficiency and lifetime. The control problems associated with automotive fuel cell systems as well as the optimization issue associated with hybrid energy systems (comprising fuel cells, batteries, and ultra-capacitors) are elaborately analyzed. The review concludes with current problems and challenges faced by the energy control systems of fuel cell vehicles.