The problems of the transportation energy and environment are the major challenges faced globally in the 21st century and are especially serious for China. The future 20 years is the strategic opportunity period of the transition of the transportation energy and powertrain system for China. The greatest characteristics of hydrogen economy lie in its diversity of the primary energy source, the unification of energy carrier and the greening of energy transformation. Development of hydrogen energy transportation powertrain system is suitable for China from the views of the situation of Chinese resources and energy sources, the urban and rural layouts, the superiority of later development and the successful practices of clean cars and electric vehicle development projects. The transition of the transportation energy powertrain system includes three parts: the transition of the energy structure, the transition of the powertrain system and the transition of the fuel infrastructure. The technical pathways of energy powertrain system transition includes expending the use of gaseous fuel to prompt the multiform of the transportation energy and to prepare for the transition of the infrastructure simultaneously, developing and promoting the hybrid technology to solve the current energy and environment problems and to prepare for the transition of powertrain system, and focusing on the research and development and demonstration of fuel cell vehicles and the hydrogen energy technology to prompt the earlier formation of the market of fuel cell vehicles. The goal in the near and medium term of transition is to reduce the fuel consumption by 100 million ton in 2020 by substituting and saving, and the long-term goal is to setup the infrastructure of hydrogen and fuel cell vehicle as the main one replacing the petroleum internal combustion engine vehicle. In order to realize the strategic goals of the transition, the four-phases strategic periods and research and development activities are discussed and proposed.