Dynamic brain networks provide a powerful representation for capturing temporal variations in functional brain connectivity and have gained increasing attention in brain disease diagnosis. However, most existing methods extract features from isolated time windows, making it difficult to capture the high-order dynamic evolution of brain activity. Moreover, these methods often neglect the functional heterogeneity among brain regions, thereby limiting diagnostic performance. To address these limitations, we propose HyperDiag, a novel temporal-regional Hypergraph learning via topology-enhanced state propagation for brain disease Diagnosis. Specifically, we first design a dual-level hypergraph learning strategy: a temporally-evolving hypergraph message passing strategy to capture dynamic high-order dependencies within and across time windows, and meanwhile, a region-wise functional hypergraph learning strategy to capture regional dependencies. Subsequently, we construct a topology-enhanced selective state-space propagation network to integrate complementary information from both the temporally-evolving and region-wise features. Extensive experiments on four brain disorder datasets (ABIDE-I, ADNI, REST-meta-MDD, and Epilepsy) demonstrate that HyperDiag not only outperforms state-of-the-art methods but also identifies biologically meaningful abnormal connections, offering potential biomarkers for clinical interpretation. Our code is available in the Appendix.