Green transportation is the core embodiment of ecological civilization and the concept of green development within the field of transportation, and it is an important strategic choice for sustainable urban development. National central cities represent the highest level in China’s urban system planning. This paper aims to evaluate the level of green transportation development in national central cities. It established a set of 29 specific evaluation indicators from five dimensions: basic indicators, green transportation infrastructure, traffic environmental protection, traffic travel, and traffic safety. It constructed an evaluation index system for the development level of green transportation. The entropy weight TOPSIS method was utilized to evaluate the development levels of green transportation in nine national central cities from 2020 to 2022. An obstacle degree model was constructed to identify key obstacle factors at both the criterion and indicator layers of the green transportation development level evaluation index system for national central cities. Suggestions were proposed from five aspects: establishing a comprehensive policy framework, promoting regional collaborative development, accelerating infrastructure construction, improving transportation service quality, and fostering the green upgrading of industries. The results showed that the comprehensive ranking of green transportation development levels among the national central cities from high to low for the years 2020–2022 was as follows: Shanghai, Chongqing, Chengdu, Beijing, Guangzhou, Tianjin, Wuhan, Xi’an, Zhengzhou. In terms of the regional spatial layout, the green transportation development levels of the nine national central cities generally exhibited a “high on the periphery, low in the center” distribution characteristic. The comprehensive ranking of the obstacle degree in the criterion layer was as follows: basic indicators, traffic travel, green transportation infrastructure, traffic environmental protection, traffic safety. After screening the criteria level where the obstacle degree calculation results are above 15%, traffic safety is eliminated. The nine cities, which were located in different regions, generally maintained consistent internal obstacle factors and their order. The top five indicators with the highest frequency of obstacle degrees at the indicator layer were as follows: total passenger transport volume, number of taxis, new energy vehicle production, expenditure for transportation, and total freight transport volume. The specific key obstacle factors at the indicator level were different in the nine cities.