Abstract Occurring in 2015/16, the strong El Niño has been shown to significantly influence the pantropical carbon fluxes with multiple lines of evidence. However, a comprehensive understanding on the regional and vegetation‐specific net ecosystem productivity (NEP) in response to this El Niño event and its recovery trajectories remain unclear. We revisited the controlling factors in the recovery of pantropical NEP from the 2015/16 El Niño until 2020 using a data assimilation framework. We estimated the pantropical net carbon emissions of 0.91 Pg C/yr in 2015 and the mean fraction of recovered area was 0.77 ± 0.07 during 2016–2020. Specifically, we found that temperature and radiation played dominant roles in controlling the recovery of forests’ NEP via reducing photosynthesis. Furthermore, we revealed the compound climatic controls on enhanced ecosystem respiration offset NEP recovery over non‐forests. These results suggest that the divergence in carbon fluxes regulates the pantropical ecosystem net carbon uptake recovery.