In order to reveal the law of flood evolution in the lower reaches of Nenjiang River and its impact on the vegetation in the floodplain, a one and two-dimensional hydrodynamic coupling model from Jiangqiao to Dalai river section was established using MIKE FLOOD. The measured data during the flood seasons of 1998 and 2013 were selected to calibrate and verify the roughness of the river section, and the flood process in typical river section with four different return periods were simulated. Based on the MOD13Q1 data set of the MODIS satellite from 2000 to 2019, the vegetation indices(NDVI, EVI)of the submerged range of different flood frequencies were obtained, and the impact of flood disturbances in the lower reaches of Nenjiang River in different return periods on vegetation was evaluated. The results show that the simulation effect of the model during the calibration and verification period meets the accuracy of Class A prediction, and the simulation accuracy of the model is high. The vegetation index in different return periods has a strong seasonal variation, and floods have obvious destructive effects on vegetation. The destructive effect has a relatively short periodicity in Nenjiang River Basin, indicating that the vegetation in this area is highly recoverable. At the same time, affected by the degree of frequent flooding, the vegetation index of different return periods conforms to the moderate interference hypothesis.