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Recent research has revealed that the dynamics of autumn phenology play a decisive role in the inter-annual changes in the carbon cycle. However, to date, the shifts in autumn phenology (EGS) and the elements that govern it have not garnered unanimous acknowledgment. This paper focuses on the Yellow River Basin (YRB) ecosystem and systematically analyzes the dynamic characteristics of EGS and its multiple controls across the entire region and biomes from 1982 to 2015 based on the long-term GIMMS NDVI3g dataset. The results demonstrated that a trend toward a significant delay in EGS (p < 0.05) was detected and this delay was consistently observed across all biomes. By using the geographical detector model, the association between EGS and several main driving factors was quantified. The spring phenology (SGS) had the largest explanatory power among the interannual variations of EGS across the YRB, followed by preseason temperature. For different vegetation types, SGS and preseason precipitation were the dominant driving factors for the EGS in woody plants and grasslands, respectively, whereas the explanatory power for each driving factor on cultivated land was very weak. Furthermore, the EGS was controlled by drought at different timescales and the dominant timescales were concentrated in 1–3 accumulated months. Grasslands were more significantly influenced by drought than woody plants at the biome level. These findings validate the significance of SGS on the EGS in the YRB as well as highlight that both drought and SGS should be considered in autumn fall phenology models for improving the prediction accuracy under future climate change scenarios. [ABSTRACT FROM AUTHOR]