Understanding how historical flooding duration and contemporary extreme flooding events interact to affect the ecosystem processes is necessary to develop biochemical models and accurately predict ecological functions in the future. In this study, we focused on the nitrogen (N) removal processes of riparian ecosystems (i.e., denitrification and anammox rates), and simulated the short-term flooding events with three different frequencies across three altitude zones. Each zone is subjected to a certain flooding duration for a decade. In addition, a meta-analysis including 2797 data points among different ecosystems was conducted to investigate the relationship between denitrification and anammox processes. The results show that altitude impacts the response of riparian ecosystem processes to short-term flooding events. With the altitude increase, the response ratio of N removal processes shifted from negative to positive, owing to the change of soil nutrients, microbial diversity, carbon and N content in leaf and root. Moreover, the coupled relationship between denitrification and anammox rates was typically found at topsoil, which can be attributed to the obvious link between denitrifies and anammox process. The pH, soil temperature, available carbon and N were the dominant drivers for their relationship. Furthermore, leaf N and root carbon indirectly impacted the response of anammox rate to extreme flooding frequency via altering the diversity of norB/C, nirD, and narH/G. Leaf carbon and root N indirectly impacted the response of anammox rate to moderate flooding frequency via altering the diversity of hao and narH/G. Upscaling the result to the riparian zone of Three Gorge Reservoir, 4.8 × 105 t N year-1 could be removed, and the highest N removal efficiency (2.0 × 105 t N year-1) was observed at the low altitude. This study highlights the flooding duration in regulating nitrogen removal function, which should be taken into account in the ecological process models and help to accurately predict the ecosystem functions.