With the booming freight industry in China in recent years, the freight volume has presented a growing trend, but the accompanied motor vehicle pollution emission becomes increasingly prominent. For the purpose of green development in freight industry, China is taking active measures to reduce emissions. Among them, the structural emission reduction enjoys the greatest potential in energy conservation and emission reduction in the transportation industry in the future. Its key is to adjust the current unreasonable transportation structure in China, and promote the transfer of freight transport from road to rail and water through the development of multimodal transport. Therefore, systematically finding out the structural characteristics of China’s freight industry and sorting out the problems existing in the freight structure can provide technical support for promoting the structural emission reduction of the freight industry and building an intensive, efficient and green cargo transportation system. This study systematically analyzed the overall development and structural characteristics of China’s freight transportation, calculated the current situation and characteristics of CO2 emissions in China’s freight transportation sector, summarized and analyzed the main problems facing energy conservation and emission reduction in China’s freight transportation sector, and put forward countermeasures and suggestions.