Popularity bias challenges recommender systems by causing uneven recommendation performance and amplifying the Matthew effect. Limited user-item interactions confine unpopular items within embedding neighborhoods of few users, leading to representation collapse and reduced model generalization. Existing supervised alignment and reweighting methods mitigate this bias but have key limitations: (1) ignoring inherent variability across Graph Convolutional Networks (GCNs) layers, causing negative effects in deeper layers; (2) reliance on fixed hyperparameters to balance item popularity, restricting adaptability and increasing complexity. To address these issues, we propose the Graph-Structured Dual Adaptation Framework (GSDA). Our theoretical analysis identifies a crucial limitation of supervised alignment methods caused by over-smoothing in GCNs. As GCN layers deepen, popular and unpopular items increasingly lose distinctiveness, quantified by reduced conditional entropy. This diminished distinctiveness weakens supervised alignment effectiveness in mitigating popularity bias. Motivated by this, GSDA captures structural and distribution characteristics from the adjacency matrix through a dual adaptive strategy. First, a hierarchical adaptive alignment mechanism uses the adjacency matrix's Frobenius norm for layer-specific weight decay, countering conditional entropy reduction effects at deeper layers. Second, a distribution-aware dynamic contrast weighting strategy, guided by a real-time Gini coefficient, removes dependence on fixed hyperparameters, enabling adaptability to diverse data. Experiments on three benchmark datasets demonstrate GSDA significantly alleviates popularity bias and consistently outperforms state-of-the-art recommendation methods.