Quantitative analysis on decoupling between economic output, carbon emission, and the driving factors behind decoupling states can serve to make the economy grow without increasing carbon emission in China’s transport sector. In this work, we investigate the decoupling states and driving factors of decoupling states in the transport sector of China’s four municipalities (Beijing, Shanghai, Tianjin, and Chongqing) through combining the Tapio decoupling approach with the decomposition technique. The results show that (i) the decoupling state of Beijing, Shanghai, and Tianjin improved; Beijing stabilized in weak decoupling; Shanghai and Tianjin appeared to have strong decoupling, but the decoupling state of Chongqing deteriorated from decoupling to negative decoupling. (ii) The energy-saving effect was the primary contributor to decoupling in these four municipalities, promoting transport’s economic growth strongly decouple from carbon emission. The economic scale effect was not optimized enough in Chongqing, facilitating expansive coupling, and expansive negative decoupling emerged. But it had a rather positive impact on decoupling process in Beijing, Shanghai and Tianjin, promoting economic growth to weakly decouple from carbon emission. (iii) The carbon-reduction effect promoted strong decoupling, which emerged in Shanghai’s transport sector, more so than in the other three municipalities, in which weak decoupling emerged. Finally, several relevant policy recommendations were offered to promote the decoupling of carbon emission from economic growth and low-carbon transport.