Atmospheric aerosols in megacities impact air quality and public health. However, limited information exists on the detailed molecular composition of organic aerosols in urban areas. This study characterized the molecular composition of organic aerosols (OA) in Shanghai, Beijing and Guangzhou, China, during summer and winter of 2021. Liquid chromatography-orbitrap mass spectrometry detected 4536−5560 and 2067− 3489 organic molecular formulas in positive (ESI+) and negative (ESI−) electrospray ionization modes, respectively. CHO and CHON compounds accounted for over 80% and 60% of total abundance in ESI+ and ESI−, respectively, suggesting their significant contribution to urban OA. The number and abundance percentages of CHO showed obvious seasonal variation, with more CHO in summer than in winter, while CHON exhibited the opposite trend in Beijing and Shanghai. Compared with winter, a lower unsaturation degree, reduced aromaticity, and higher oxidation state of OA in summer were observed in Beijing and Shanghai, while these seasonal variations were not as obvious in Guangzhou, likely due to regional climate differences. The number percentage of common compounds between Beijing and Shanghai was higher than that between Guangzhou and Beijing (or Shanghai). Nitroaromatic compounds were more prevalent in winter than in summer. Further analysis of atmospheric formation relevance and precursor-product pairs suggested that CHON compounds are derived from the oxidization or hydrolyzation processes, revealing potential chemical transformations of these aerosols. This study characterized the chemical makeup of organic aerosols, providing insight into their sources and characteristics in these cities.