The Yellow River Basin is an important ecologically vulnerable region in China. The response of vegetation growth to climate change and drought stress in this region requires urgent clarification. This study aims to investigate the differential inhibitory effects of drought on carbon uptake across 15 ecosystems and to examine the mechanisms underlying these changes. In our analyses, we used multiple methods, including trend analysis, structural equation modeling (SEM), and ridge regression, and integrated multi-source remote sensing data, including the Standardized Precipitation Evapotranspiration Index (SPEI), precipitation (Prec), and temperature (Ta). The results indicate that: (1) Grassland GPP showed widespread declines in the middle and lower reaches, suggesting that grasslands were the most sensitive to drought stress. (2) Grasslands primarily exhibited lagged responses of 4 months, whereas croplands responded with shorter, 1-month lags. In contrast, Forests showed cumulative responses over 10-12 months. Additionally, high-resilience croplands were expanding along the Henan-Shandong axis. Forest resilience was lowest in the semi-arid northwest region and in Ningxia across the basin. (3) Prec was identified as the primary positive driver of basin-wide GPP. Grassland GPP was directly regulated by Prec, whereas cropland GPP was mainly limited by photosynthetically active radiation (PAR), although soil moisture (SM) could mitigate drought stress. In forest ecosystems, vapor pressure deficit (VPD) was the key limiting factor, and elevated Ta intensified the negative effects of drought by reducing SM. This research will contribute to strengthening future ecosystem management and mitigating the threats of climate change to ecosystems.