As Earth's warming is driven by anthropogenic activities (e.g., urbanization), land and ocean warming significantly affect the net carbon uptake (NCU) of global ecosystems. However, the driving mechanism of coupled land-sea warming on the NCU under rapid urbanization in coastal areas remains poorly understood. Here, we used long-term remote sensing and meteorological observation data combined with spatial analysis and multivariate statistical methods to study the impact of coupled land-sea warming and urbanization on land net primary productivity (LNPP, a proxy of the net land carbon uptake) in the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), a rapidly urbanizing and climatically vulnerable area of South China. We found that the total LNPP decreased by 0.40 TgC from 1985 to 2015 and declined suddenly after 2003, driven by the reduced relative humidity and increased vapor pressure deficit (VPD). The increased VPD was caused by coupled land-sea warming, and the indirect effect (γ = −0.51, p < 0.001) of coupled land-sea warming on LNPP variability was much stronger than the direct effect (γ = −0.16, p < 0.05). In addition to the severe decline in the LNPP (0.20 TgC) induced by coupled land-sea warming, urbanization caused a large loss in LNPP (0.16 TgC), which accounted for 40% of the total LNPP loss. Our findings can support future predictions of regional carbon uptake and inform future climate change mitigation strategies to implement carbon peak and neutrality goals.