The Amazon, the Earth's largest tropical forest, plays a critical role in the global carbon cycle, acting as a significant carbon sink. Recent studies, however, indicate a decline in its carbon sequestration capacity due to climate variability, intensive deforestation, and fires. This study aims to examine the impacts of these factors on the carbon dynamics of the Amazon over a centennial scale based on dynamic global vegetation models (DGVMs) of Trendy-v11. It was found that the Amazon region exhibited significant spatiotemporal variations in net land carbon (C) fluxes, and was a net C sink (40.02 ± 242.64 Tg C yr−1) during 1901–2021. The Amazonian net biome productivity (NBP) showed a 6-decades-scale shift from a decreasing trend (−3.78 Tg C yr−2) during 1901–1959 to an increasing trend (2.39 Tg C yr−2) during 1960–2021. The Amazonian NBP was negatively related to air temperature while positively related to dry-season precipitation during 1901–2021. Furthermore, the increase of atmospheric CO2 concentration during 1901–2020 enhanced Amazonian NBP by 36.40 ± 8.39 Pg C, which was largely offset by land use change (−18.84 ± 12.02 Pg C) and climate change (−10.03 ± 5.00 Pg C). Our findings underscore the critical need for sustainable management practices in the Amazon to enhance its C sink and preserve its function in the global climate system.