A source-oriented Community Multiscale Air Quality model was used to quantify the contributions of different sources to ground-level fine particulate matter (PM2.5) and ozone (O3) over the Yangtze River Delta (YRD) region during the EXPLORE-YRD (EXPeriment on the eLucidation of the atmospheric Oxidation capacity and aerosol foRmation, and their Effects in the Yangtze River Delta) campaign (17 May to June 17, 2018). O3 formation in most urban areas of YRD is attributed to volatile organic compounds (VOCs) (81.1%, 78.5%, 60.2%, and 55.1% in Shanghai, Nanjing, Hefei, and Hangzhou, respectively), but is affected more by nitrogen oxides (NOx) in suburban and rural areas. Industry and transportation are the two major sources of O3 and PM2.5. In addition to the two sources, NOx produced owing to power generation, and VOC emissions from biogenic sources are important source of O3. Industry contributes the most to the total mass of PM2.5 in the YRD during the study period (9–25 μg/m3), followed by transportation (2–7 μg/m3). Industry, residential emissions, and transportation are the major sources of primary organic carbon and elemental carbon, whereas industry, transportation, and power generation account for most of the sulphate (SO2− 4) and nitrate (NO− 3) in the YRD. Agriculture is the most dominant source of ammonium emissions (NH+ 4). In Shanghai, Nanjing, Hefei, and Taizhou, secondary organic aerosol (SOA) are mainly contributed by industrial emissions. However, in Hangzhou, biogenic emissions contribute more than 40% of SOA. During all types of pollution episodes, industry and transportation are generally the two greatest sources of O3 and PM2.5 in YRD. The contribution of industry is higher during high PM2.5 pollution episodes, whereas biogenic and open burning contributions are more important during high O3 episodes. Overall, anthropogenic sources dominate the formation of O3 and PM2.5 pollution in the YRD, whereas biogenic emissions contribute significantly to O3 attributable to VOC emissions (O3_VOCs) accounting for 9–20% in urban areas of the YRD.