The Comprehensive Air Quality Model with extensions (CAMx), a 3-D regional chemical transport model, was used to simulate ozone concentrations in the Pearl River Delta (PRD) in November, 2009. Ozone Source Apportionment Technology (OSAT) was applied to investigate sources of two typical ozone episodes and a clean day as comparison. The results showed that emissions from urban Guangzhou and Dongguan mainly contributed to local areas and the southwestern part of PRD (15–30 μL/m3), while emissions from Shenzhen Baoan district (15–25 μL/m3) mainly affected the Pearl River Estuary. Mobile sources and solvent usage sources were two major contributors to ozone formation and had an influence in most areas of the central and western PRD. Mobile sources could contribute as much as 50 μL/m3 hourly ozone concentration to the boarding area of Foshan and Guangzhou. Trans-boundary import of ozone made episodes more likely to occur in PRD under unfavorable weather conditions, however, the ozone precursors emitted within the PRD region were the main cause of high ozone concentrations during ozone episodes. As a result, the strategies on controlling emissions within the PRD region are the key to the reduction of ozone pollutions in PRD.