Phenological changes in forests directly influence the spatiotemporal dynamics of carbon fixation and the carbon and water cycles in terrestrial ecosystems. Previous studies have shown that variations in biological factors (e.g., canopy height, leaf area, water use efficiency) can increase uncertainty in forest phenology, and these variations are closely linked to tree species and forest age-class structure. However, the interaction mechanisms through which tree species and forest age-class structure influence phenological changes remain insufficiently explored. In this study, phenological changes and their interactions and response mechanisms to different dominant tree species and forest age-class structures were analyzed via Sentinel-2 normalized difference vegetation index (NDVI) time series data from 2020 and 2021 across 480 typical deciduous forest plots in northeastern China. The results were as follows: (1) There were significant differences (p < 0.05) in the intra-annual phenological responses of temperate deciduous landscapes to the interaction between tree species and forest age-class structure. (2) The indirect effect of forest age-class structure through tree species on phenology exceeded the indirect effect of tree species through forest age-class structure, with a difference of 30.77%–35.09%. (3) When the dominant tree species and forest age-class structure were not distinguished, phenological differences in temperate forests ranged from 3 to 41 days and 2 to 23 days, respectively. This study highlights the differential impacts of key biological factors and their interactions on regional forest phenology, offering valuable insights into how these factors influence forest landscapes and providing a theoretical basis for improving forest management strategies.