The net ecosystem exchange (NEE), determining terrestrial carbon sequestration capacity, is strongly controlled by climate change and has exhibited substantial year-to-year fluctuations. How the increased frequency and intensity of warm extremes affect NEE variations remains unclear. Here, we combined multiple NEE datasets from atmospheric CO2 inversions, Earth system models, eddy-covariance data-driven methods and climate datasets to show that the terrestrial carbon sequestration capacity is weakened during warm extreme occurrences over the past 40 years, primarily contributed by tropical regions (81% ± 48%). The underlying mechanism can be rooted in the overwhelmingly decreased trend of gross primary productivity compared with terrestrial ecosystem respiration. Additionally, the weakened terrestrial carbon sequestration capacity is mainly driven by the transition from temperature or soil moisture control to vapour pressure deficit control, which is associated with the increasing intensity of warm extremes. Our findings suggest that warm extremes threaten the global carbon sequestration function of terrestrial ecosystems. Therefore, more attention should be given to the evolution of the increasing intensity of warm extremes in future climate projections.