Reducing the amount of organic aerosol (OA) is crucial to mitigation of particulate pollution in China. We present time and air-origin dependent variations of OA markers and source contributions at a regionally urban background site in South China. The continental air contained primary OA markers indicative of source categories, such as levoglucosan, fatty acids, and oleic acid. Secondary OA (SOA) markers derived from isoprene and monoterpenes also exhibited higher concentrations in continental air, due to more emissions of their precursors from terrestrial ecosystems and facilitation of anthropogenic sulfate for monoterpenes SOA. The marine air and continental–marine mixed air had more abundant hydroxyl dicarboxylic acids (OHDCA), with anthropogenic unsaturated organics as potential precursors. However, OHDCA formation in continental air was likely attributable to both biogenic and anthropogenic precursors. The production efficiency of OHDCA was highest in marine air, related to the presence of sulfur dioxide and/or organic precursors in ship emissions. Regional biomass burning (BB) was identified as the largest contributor of OA in continental air, with contributions fluctuating from 8% to 74%. In contrast, anthropogenic SOA accounted for the highest fraction of OA in marine (37 ± 4%) and mixed air (31 ± 3%), overriding the contributions from BB. This study demonstrates the utility of molecular markers for discerning OA pollution sources in the offshore marine atmosphere, where continental and marine air pollutants interact and atmospheric oxidative capacity may be enhanced.