Cyanobacterial blooms can promote nitrogen removal; however, the underlying mechanism remains a mystery. The present study suggested that the carbon−nitrogen coupling metabolism should play a critical role in nitrogen removal in eutrophic lakes. Field investigations illustrated that the carbohydrate content of natural Microcystis negatively correlated with the DIN concentration in spatiotemporal distribution. Under N-deficient conditions, the carbohydrate content of natural Microcystis increased from 10.5% to 44.1% after 4 days. The metabolomic analysis showed ten differential carbohydrate metabolites, of which seven were upregulated. More carbohydrate-rich Microcystis biomass might sink onto the bottom under a low-nitrogen condition; thus, nitrogen was removed more efficiently due to the enhancement of denitrification. This was further supported by enclosure experiments with Microcystis in which TN was removed more efficiently under low-nitrogen conditions (40.6%) than under high-nitrogen concentrations (17.4%). These results illustrated that the carbon/ nitrogen coupling mechanisms in intracellular physiological processes of Microcystis and in lake ecosystems were tightly linked, especially since lakes suffer from eutrophication. The present study provided field evidence for carbohydrate accumulation in Microcystis at nitrogen deficiency and indicated that the cyanobacteria−carbon interactions maintain the lake's high potential to remove nitrogen via denitrification.