Abstract Cities are the major contributors to energy consumption and CO2 emissions, as well as being leading innovators and implementers of policy measures in climate change mitigation. Guangdong-Hong Kong-Macao Greater Bay Area (GBA) is an agglomeration of cities put forward by China to strengthen international cooperation among “Belt and Road” countries and promote low-carbon, inclusive, coordinated and sustainable development. Few studies have discussed the emission characteristics of GBA cities. This study, for the first time, compiles emission inventories of 11 GBA cities and their surroundings based on IPCC territorial emission accounting approach, which are consistent and comparable with the national and provincial inventories. Results show that (a) total emissions increased from 426 Mt in 2000 to 610 Mt in 2016, while emissions of GBA cities increased rapidly by 6.9% over 2000–2011 and peaked in 2014 (334 Mt); (b) raw coal and diesel oil are the top two emitters by energy type, while energy production sector and tertiary industry are the top two largest sectors; (c) GBA cities take the lead in low-carbon development, emitted 4% of total national emissions and contributed 13% of national GDP with less than a third of national emission intensities and less than three-quarters of national per capita emissions; (d) Macao, Shenzhen and Hong Kong have the top three lowest emission intensity in the country; (e) most of GBA cities are experiencing the shift from an industrial economy to a service economy, while Hong Kong, Shenzhen, Foshan and Huizhou reached their peak emissions and Guangzhou, Dongguan and Jiangmen remained decreasing emission tendencies; (g) for those coal-dominate or energy-production cities (i.e. Zhuhai, Zhongshan, Zhaoqing, Maoming, Yangjiang, Shanwei, Shaoguan and Zhanjiang) in mid-term industrialization, total emissions experienced soaring increases. The emission inventories provide robust, self-consistent, transparent and comparable data support for identifying spatial–temporal emission characteristics, developing low-carbon policies, monitoring mitigation progress in GBA cities as well as further emissions-related studies at a city-level. The low-carbon roadmaps designed for GBA cities and their surroundings also provide a benchmark for other developing countries/cities to adapting changing climate and achieve sustainable development.