Functional group diversity is fundamental to the stability and resilience of marine ecosystems. While laboratory studies suggest that distinct zooplankton feeding strategies entail different energetic trade-offs, how these behavioral traits manifest across long-term and fine-scale variations remains poorly understood in dynamic estuaries. Utilizing a comprehensive dataset from the Yangtze River Estuary, we investigated the spatiotemporal reassembly and structural stability of copepod functional groups categorized by distinct feeding modes across seasonal transitions and a decadal scale. Our analysis revealed pronounced asymmetric responses among different feeding groups. At the seasonal scale, the community exhibited a distinct successional trajectory in functional composition between spring and summer. More importantly, the decadal analysis uncovered a significant long-term structural realignment within specific seasons, indicating a potential directional shift in community complexity over the past decade. Furthermore, we identified highly contrasted, decoupled correlation patterns between specific copepod functional groups and major phytoplankton taxa, reflecting the possible field manifestation of variations in prey selection and detection mechanisms. These findings suggest that behavioral traits could potentially modulate long-term and high-resolution zooplankton community reassembly under environmental fluctuations, highlighting the value of incorporating trait-based functional diversity into evaluating estuarine ecosystem responses to global change.