In this study, imidacloprid, clothianidin and thiamethoxam were selected as model pollutants of NENIs, their accumulation, migration and metabolic characteristics in vegetables were explored through a 35-day pot experiment. The results showed that clothianidin-urea, imidacloprid-urea and imidacloprid olefin were transformed by the functional microorganisms in the soil, and these transformation products were subsequently absorbed by lettuce and carrot through the root system, then migrated to their above-ground parts. However, clothianidin-desmethyl, thiamethoxam-desmethyl and 6-chlornicotinic acid were produced by further endogenous metabolism of imidacloprid, clothianidin and thiamethoxam or their soil transformation products after they were absorbed by lettuce and carrot. Risk assessment results showed that transformation products increased NENIs risk in edible parts of lettuce and carrot by 0.57%-8.34% and 0.65%-24.64%, respectively. This study indicated that the contribution of transformation products with higher toxicity should be taken into consideration appropriately intake risk assessment of NENIs in the future.