Stable carbon and nitrogen isotopes and fatty acid compositions of Aurelia aurita, Stomolophus meleagris and Cyanea nozakii collected from the Yellow Sea in August 2009, were analysed. δ13C and δ15N values of the jellyfishes were in the range of −22.0‰ to −17.4‰ and 4.8‰ to 10.6‰, respectively, which indicated that jellyfishes in this study area were mainly dependent on marine-based carbon. The trophic levels of jellyfishes were estimated as between zooplanktons and high level carnivorous fishes. Low C18:1n-7/n-9 ratios and high C20:1 (n-11 and n-9) and C22:1 (n-11 and n-9) concentrations suggested jellyfishes in the Yellow Sea were carnivorous and zooplanktons were an important diet for them. Fatty acid compositions of jellyfishes were characterized by high C20:4n-6 concentration (>10%), with ratios of C20:5n-3/C22:6n-3 >1. Specific fatty acids (C20:1 + C22:1 and C20:4n-6) indicated that both pelagic-derived material and benthic detritus-derived food were diet of jellyfishes. Variations of certain biomarkers (C15:0 + C17:0, C20:1 + C22:1 (n-11 and n-9) and C20:4n-6) in jellyfishes of different body sizes suggested that ontogenetic diet shifts may take place during the growth of jellyfishes. Larger individuals with higher C20:1 + C22:1 (n-11 and n-9) concentration, tended to consume more zooplanktons; while the detritus-derived material made a more significant contribution to the small individuals, as suggested by higher C15:0 + C17:0 and C20:4n-6 concentrations. According to our study, besides the diet, species seemed to influence variations in stable isotopes and fatty acid compositions in jellyfishes.