As high-speed rail operations increase and extreme weather events intensify, the stability of railway subgrades faces greater risks. Previous studies often focus on direct impacts but overlook complex interactions. Here, we use structural equation modeling to examine the relationships between climate, land use, geomorphology, geology, spatial factors, and operational characteristics influencing subgrade defects in China’s high-speed rail system. Data used in this study were obtained from official documents and open-source databases, including land types, subgrade defects, and weather patterns. Our results show that land types like sandy and bare lands contribute to subgrade defects. Both geomorphology and operational characteristics play key roles, with geomorphology affecting subgrade stability indirectly. Bare land influences settlement and uplift deformation, while frost damage and mud pumping are driven by freezing days and rainfall. Projections indicate that the risk of subgrade defects will increase in the future, underscoring the need for proactive resilience measures. © 2025 Elsevier B.V., All rights reserved.