PM2.5-bound n-alkanes in Shanghai (SH), Nanjing (NJ) and Ningbo (NB) cities from November 2014 to August 2015 were investigated. Averaged concentrations of the total 25 n-alkanes (∑n-alkanes, C16–C40) in SH, NJ and NB were 97.4 ± 73.9, 83.8 ± 57.1 and 187.1 ± 87.1 ng m–3, respectively. Obvious spatial and seasonal variations were attributed to the differences of emission sources and meteorological conditions. Analysis of the diagnostic ratios and specific molecular markers of n-alkanes suggested that high plant wax and vehicle emissions were the major sources of n-alkanes in the YRD region. Strong inputs of microbial components in summer were found and attributed to the emission from plankton in the ocean. The annual average contributions of higher plant wax to n-alkanes (%wax) in SH, NJ and NB were estimated to be 47.5%, 50.1% and 34.5%, respectively. Anthropogenic sources were responsible for the n-alkanes in NB, while biogenic sources contributed much more n-alkanes in NJ and SH. Based on the result of backward analysis, the emissions of n-alkanes in NB and NJ were mainly from local sources when the air masses came from the sea and south China with low n-alkanes concentrations. When the air masses originated from north China, the transport of contaminant aggravated the pollution of n-alkanes in SH.