In most emissions scenarios consistent with the temperature targets of the Paris Agreement, carbon dioxide removal (CDR) would be required to achieve net negative emissions. The efficiency of CDR depends on the behavior of the natural carbon reservoirs, land and ocean, that regulate atmospheric CO2 concentrations, but their change in response to negative emissions is highly uncertain. Here, we investigate the response of the terrestrial and oceanic carbon cycle to negative emissions based on an idealized emission-driven simulation using a state-of-the-art Earth system model. The terrestrial and oceanic carbon sinks become carbon sources ~30 years after the onset of negative emissions. Thereafter, although the atmospheric CO2 concentration returns to its initial level, the terrestrial ecosystem and the ocean continue to release carbon. The ocean recovers as a carbon sink within a few decades, while the terrestrial ecosystem remains a carbon source until the end of the simulation. The prolonged carbon emissions from the land are due to the delayed response of respiration to the earlier increase in terrestrial carbon uptake. As a result, the total carbon stock on land gradually decreases but still remains higher than its initial state. The ocean carbon inventory shows an irreversible change within a few centuries due to the accumulation of anthropogenic CO2 in the deep ocean, which would take more than centuries to be removed naturally.