Autumn phenology plays a critical role in shaping the carbon sequestration capacity of temperate forests. Notable local-scale variations in autumn phenology have drawn increasing attention recently, potentially introducing substantial uncertainty when predicting temperate forest productivity. Yet the underpinning mechanisms driving these variations remain inadequately elucidated. Here we observed significant and consistent relationships between canopy structure and autumn phenology across six temperate forest sites, induced by the regulation effect of canopy structure on microclimate conditions. Incorporating the identified ‘canopy structure–microclimate–autumn phenology’ pathway into existing autumn phenology models significantly improves the prediction accuracy and reduces the projected delay in the start of autumn over the remainder of the century. These findings offer a new perspective for interpreting the local variations of autumn phenology in temperate forests and emphasize the urgent need to integrate the identified pathway into the Earth system and vegetation models, especially considering the asynchronous changes of macroclimate and microclimate conditions.