As a new alternative fuel vehicle for energy reserve strategy, the development of methanol vehicles in China has been at the forefront. Completed pilot projects have demonstrated that methanol vehicles can effectively reduce fuel costs and pollutant emissions during driving. In addition to methanol vehicles, alternative fuel vehicles such as electric vehicles and compressed natural gas vehicles also maintain a sound development momentum in China. It is essential to understand which one has more advantages from sustainable development. This paper uses the Energy, Environment, and Economy (3E) evaluation method to analyze the energy consumption, environmental emission, and economy of methanol, electric, gas, and gasoline vehicles from the whole life cycle perspective. A comprehensive index evaluation model was constructed, and the development potential of the three alternative fuel vehicles was ranked under four different scenarios (energy-oriented, environment-oriented, economic-oriented, and equilibrium scenarios). This research shows that methanol vehicles have higher total energy consumption than gasoline vehicles in the whole life cycle. In terms of greenhouse gas emissions, compared with gasoline vehicles, methanol, and compressed natural gas vehicles decreased by 8.79 tons and 12.45 tons, respectively. At the same time, methanol vehicles have a better economic benefit than gasoline vehicles (37%), which is the same as the completed pilot projects. In addition, results also show that due to the advantages of low renovation cost and fuel price, the user’s cost of methanol vehicles is more down than blade electric vehicles, which makes them have better development potential compared with electric and compressed natural gas vehicles in the economic-oriented and equilibrium scenario. Therefore, methanol vehicles can be used as alternative fuel vehicles for long-term development in China.