Habitat degradation and alien species invasion are the main threats for freshwater ecosystem. Therefore, quantifying the differences of diet composition between alien invasive and native species under different human disturbance intensities is very important for the understanding of the intensity of interspecific competition and determining appropriate management strategies. In this study, stable carbon and nitrogen isotope analysis technique was used to compare the diet composition and variations between the invasive species of Procambarus clarkii and the native species of Macrobrachium nipponense at open water (nature) and black poplar (Populus nigra) plantation (modified) wetlands in the West Dongting Lake. Ninety-one samples of consumers and potential food sources were collected between August 8 and 18, 2017. Bayesian mixture model were used to estimate diet composition of P. clarkii and M. nipponense at the two types of wetland. Result showed that compared with natural wetland, the number of P. clarkii in the modified wetland was larger and the diet overlap between invasive species (P. clarkii) and native species (M. nipponense) was greater in the modified wetland than in the natural wetland. Compared with P. clarkii, the native specie (M. nipponense) consumed more animal food in natural wetland. In the modified wetland, the δ¹³C for both P. clarkii and M. nipponense increased significantly, and their diet contained higher proportion of plant food sources. However, only M. nipponense showed significant changes in δ¹⁵N, while δ¹⁵N of P. clarkii showed no significant changes between the two habitats. This study suggested that with the increase of human disturbance, the impact of alien invasive organisms on local organisms increased.