Abstract The three metropolitan regions, including Jing-Jin-Ji (JJJ), Yangtze River Delta (YRD) and Pearl River Delta (PRD), are the most developed regions of China. This study focuses on these three metropolitan regions and tries to estimate and analyze the structure and influencing factors of $ CO_{2} $ emissions from transport sector, including passenger and freight transport, simultaneously covering road, rail, and water transport. The results suggest that in the period of 2000–2013, the $ CO_{2} $ emissions from transport sector increased from 27.8 to 198.8 Mt in JJJ, from 29.7 to 163.5 Mt in YRD, and from 13.1 to 74.0 Mt in PRD. Comparatively speaking, JJJ had the highest $ CO_{2} $ emission intensity of freight and urban passenger transport as well as highest transport $ CO_{2} $ emissions per capita and per unit GDP, while PRD had the highest transport $ CO_{2} $ emissions per hectare. The main challenge of reducing $ CO_{2} $ emissions from transport sector in these regions stemmed from freight transport and road transport. Based on decomposition analysis, economic welfare was the most important driving force of the $ CO_{2} $ emissions growth in all three regions, followed by transport type mix, transport dependence and modal energy intensities. In the future, low-carbon transport strategies about controlling the growth of transport demand, adjusting the transport modal structure and improving the modal energy efficiency and fuel emission efficiency are needed in all three regions, and each region should have slightly different focus. The JJJ region needs to emphasize adjusting transport modal structure, the YRD region needs to emphasize improving modal energy efficiency, and the PRD region needs to focus more on controlling the growth of transport dependence.