Invasive plants strongly affect physical and biotic environments of native ecosystems. Insects and other arthropods as one of the major components of many ecosystems are very sensitive to subtle changes in abiotic and biotic environments. We examined the effects of exotic Spartina alterniflora invasion on community structure and diets of arthropods in a saltmarsh previously dominated by native Phragmites australis in Yangtze River stuary through net sweeping and plant harvesting methods and stable isotope analysis. Our results showed that diversity indices were not significantly different between exotic and native plant communities, but the total abundance of insects estimated through plant harvesting method was found to be lower in Spartina monoculture than that in Phragmites monoculture. Community structure of insects in Spartina monoculture was dissimilar to that in Phragmites monoculture and Phragmites–Spartina mixture. Moreover, stable carbon isotope patterns of arthropods were significantly different between Phragmites and Spartina monocultures. Although some native arthropods (perhaps generalists) shifted their diets, many native taxa did prefer Phragmites to Spartina even in Spartina monoculture. Spartina invasions resulted in reduced abundances of some arthropds, and increased dominance of others feeding preferably on Spartina. This study provides vidence that invasive plants can change the community structure and diets of native arthropods, which will eventually alter the arthropod food web, and affect the integrity and functioning of native ecosystems within a nature reserve that has been set aside for conserving the native biodiversity and maintaining the ecosystem integrity. In this sense, Spartina invasions in the Yangtze River estuary need to be managed appropriately.