The high-speed rail network plays a crucial role in the development of the national economy and national defense, and assessing its resilience is of great significance for ensuring transportation safety and supporting emergency decision-making. To address the limitations of traditional complex network models in capturing multifaceted, higher-order interactions, this paper constructs a high-speed rail transport hypernetwork model based on hypergraph theory and evaluates the resilience of the high-speed rail transport hypernetwork from two dimensions: hypernetwork structure and hypernetwork function. By conducting experiments on the sequential failure of design nodes, this study compares the performance evolution and resilience boundaries of high-speed rail transport supernetworks under scenarios involving random and targeted attacks, thereby providing a theoretical basis for optimizing the resilience of high-speed rail transport networks. This study focuses on the high-speed rail network in the middle reaches of the Yangtze River and conducts an empirical analysis based on data from 1,085 high-speed rail services operating on October 22, 2025. The results indicate that structural resilience is superior to functional resilience, and that networks exhibit greater resilience against random attacks than against targeted attacks. A small number of core nodes handle the network’s primary functions; if they fail, network performance will decline significantly. Attacks based on betweenness centrality are the most destructive, while those based on sub-hypergraph centrality are relatively the least destructive. Hypergraph-based hypernetworks can effectively account for the operational relationships among high-speed trains, capture the association patterns between nodes, and provide a more accurate theoretical approach for modeling high-speed rail transport networks. This paper employs hypergraph theory to construct a hypernetwork of high-speed rail transportation, taking full account of the operational relationships among high-speed train services to enhance the accuracy of research on network resilience. This paper provides a theoretical framework for assessing and enhancing the resilience of high-speed rail networks and is of great significance for promoting the sustainable development of the railway sector.