Methacrolein (MACR) and methyl vinyl ketone (MVK) are two major intermediate products from the photochemical oxidation of isoprene, the most important biogenic volatile organic compound. In addition, MACR and MVK have primary emissions. Investigating the sources and evolution of MACR and MVK could provide helpful information for the oxidative capacity of the atmosphere. In this study, hourly measurements of isoprene, MACR, and MVK were conducted at a receptor site in the Pearl River Delta region (PRD), i.e., the Heshan site (HS), from 22 October to 20 November, 2014. The average mixing ratios of isoprene, MACR and MVK were 151 ± 17, 91 ± 6 and 79 ± 6 pptv, respectively. The daily variations and the ratios of MVK/MACR during daytime and nighttime suggested that other sources besides isoprene photooxidation influenced the MACR and MVK abundances at the HS. Positive matrix factorization was utilized to resolve the sources of MACR and MVK. Five sources were identified and quantified, including biogenic emissions, biomass burning, secondary formation, diesel, and gasoline vehicular emissions. Among them, secondary formation made the greatest contribution to observed MACR and MVK with average contributions of ~ 45% and ~ 70%, respectively. Through the yields of secondary products from the oxidation of MACR and MVK by the OH radical and the concentrations of MACR and MVK, it was found that methylglyoxal and formaldehyde were the main oxidation products of MACR and MVK at the HS site. Overall, this study evaluated the roles of primary emissions on ambient levels of MACR and MVK and advanced the understanding of photochemical oxidation of MACR and MVK in the PRD.