Surface water, heat and carbon fluxes are critical indicators of the water and carbon cycles in lake ecosystems in a changing climate. However, the impact of extreme environmental conditions, such as drought, on these processes is not fully understood. Lake Poyang, the largest freshwater lake in China, is also an internationally important wetland. It is not only a key node for regulating water resources in the Yangtze River Basin, but also plays an important role in the global carbon and water cycles. In 2022, consecutive meteorological drought events occurred in the Lake Poyang Basin during the summer and autumn, and the lake area experienced its most severe drought since 1949. This study adopted multi-year monitoring data from the eddy covariance instrument at the Lake Poyang Wetland Observation and Research Station. Located on the beach of Lake Poyang (29°27'N, 116°03'E), the station has continuously monitored the variation processes of water, heat and carbon fluxes in the lake since 2015. This study analyzed the variation patterns of the water, heat and carbon fluxes, and how they responded to the extreme drought event in Lake Poyang in 2022. The results showed that: (1) On an annual scale, the latent heat flux was relatively high from July to September, peaking in August, with an annual average of 49.5 W/m2. The sensible heat flux was relatively high from September to November, peaking in October, with an annual average value of 10.6 W/m2. The CO2 flux exhibited obvious seasonal variations, with the carbon source and carbon sink shifting in response to hydrometeorological factors such as the water level and net radiation. The annual average value of the CO2 flux was 15.0 μmol/(m2·s). (2) On a daily scale, the sensible and latent heat fluxes were essentially synchronous, exhibiting a single peak at noon, whereas the CO2 flux exhibited a single peak at night. (3) The extreme drought event significantly intensified the carbon source effect of the wetland ecosystem by altering the pattern of energy allocation. During the drought period, the latent heat flux, sensible heat flux and CO2 flux increased to 1.23, 1.78 and 5.44 times the average values for the same historical period, respectively. (4) Correlation analysis revealed that air temperature, wind speed, net radiation, precipitation, relative humidity, normalized difference vegetation index (NDVI) and water level were the main factors influencing the water-heat-carbon fluxes. Stepwise regression analysis further revealed the mechanisms by which various factors influenced the fluxes under different periods and underlying surface conditions. During the extreme drought period when the underlying surface was a body of water, the ranking of importance of the influencing factors for latent heat flux, sensible heat flux and CO2 flux was as follows: wind speed > air temperature > relative humidity > net radiation > water level. When the underlying surface was a beach, the ranking of importance of the influencing factors for latent heat flux, sensible heat flux and CO2 flux was as follows: air temperature > wind speed > NDVI > vapor pressure deficit > precipitation. The extreme drought event primarily promoted energy allocation to sensible heat flux by increasing air temperature, wind speed and net radiation, and significantly stimulated CO2 release. This study revealed the response mechanisms of water-heat-carbon fluxes in lakes to extreme climate events, providing a scientific basis for predicting the responses of lake ecosystems to future climate change.