Hyperspectral imaging (HSI) plays a pivotal role in modern agriculture by capturing fine-grained spectral signatures that support crop classification, health assessment, and land-use monitoring. However, the transition from raw spectral data to reliable semantic understanding remains challenging—particularly under fragmented planting patterns, spectral ambiguity, and spatial heterogeneity. To address these limitations, we propose UniHSFormer-X, a unified transformer-based framework that reconstructs agricultural semantics through prototype-guided token routing and hierarchical context modeling. Unlike conventional models that treat spectral–spatial features uniformly, UniHSFormer-X dynamically modulates information flow based on class-aware affinities, enabling precise delineation of field boundaries and robust recognition of spectrally entangled crop types. Evaluated on three UAV-based benchmarks—WHU-Hi-LongKou, HanChuan, and HongHu—the model achieves up to 99.80% overall accuracy and 99.28% average accuracy, outperforming state-of-the-art CNN, ViT, and hybrid architectures across both structured and heterogeneous agricultural scenarios. Ablation studies further reveal the critical role of semantic routing and prototype projection in stabilizing model behavior, while parameter surface analysis demonstrates consistent generalization across diverse configurations. Beyond high performance, UniHSFormer-X offers a semantically interpretable architecture that adapts to the spatial logic and compositional nuance of agricultural imagery, representing a forward step toward robust and scalable crop classification.