ABSTRACT The Chinese mitten crab (Eriocheir sinensis) is the largest estuarine invertebrate and one of the most important fishery resources in China. Diet significantly affected survival of the crab. To study the diet of this species during its upstream migration, larvae and juvenile crabs as well as their potential food sources were sampled from three regions along the Changjiang River. Stable isotopes (δ13C and δ15N) in and fatty acid compositions of the samples were analysed to elucidate the crabs’ dietary shift during upstream migration. With upstream migration from the Changjiang Estuary, the average δ13C value in crabs decreased from −20.6 to −25.2‰, and the δ15N value increased from 3.0 to 11.8‰. The fatty acid compositions also changed significantly, with levels of C20:4n-6, C18:2n-6, and C18:3n-3 increasing during upstream migration. However, the levels of C15:0, C17:0, C16:1n-7, and 20:1n-9 exhibited the opposite trend. Pelagic marine prey items (e.g. zooplankton and bacteria) were the dominant food sources of megalopae and early juvenile crabs. The contribution of benthic terrigenous origin carbon sources (e.g. macrophytes and zoobenthos) to the juvenile crab diet sharply increased. The dietary information on the Chinese mitten crab can promote the restoration of wild population and sustainable development of crab aquaculture.