Although increasing attention is drawn to particulate air pollution across the Taiwan Strait, few studies have focused on the organic component, which comprises a large portion in ambient aerosols. Synchronous observations were conducted at seven sites in Taiwan and Fujian to explore the chemical properties and source contributions of organic aerosols across the Taiwan Strait. In total, 134 organic matters were quantified by gas chromatography–mass spectrometry. Compared to other areas in China, the proportions of n-alkanes and PAHs in the quantified organic constituent were relatively lower across the Taiwan Strait, with alkanoic acids and dicarboxylic acids higher, indicating less primary source contribution and more secondary formation influence. The chemical mass balance (CMB) model showed that cooking and vehicle emissions were the richest primary sources of organic carbon (OC) across the Taiwan Strait, accounting for 21% and 15% on average, followed by biomass burning and vegetative detritus. Coal burning had little influence in early summer across the Taiwan Strait. The percentages of diesel vehicle contributions were higher at sites in Taiwan than in Fujian, which was also verified by a higher elemental carbon (EC) to OC ratio. The contribution of biomass burning increased significantly when large amounts of fire points observed across the Taiwan Strait. This work highlights the chemical characteristics of organic aerosols and the interaction of particulate air pollution across the Taiwan Strait in a typical monsoon transition case. Sources of OC and potential origin areas of PM2.5 were also investigated to support cross-strait pollution control policies.