Abstract Against the backdrop of climate change, resource competition, and increasing socio-economic uncertainty, the resilience of the water-energy-food nexus (WEFN) has emerged as a critical issue for ensuring China’s transition toward steady development. As a representative region of China’s water-energy-food nexus (WEFN), the Yellow River Basin exhibits significant spatial disparities. Developing a theoretical framework that is better adapted to regional characteristics and examining the historical evolution and future trends of WEFN resilience (WEFNR) spatial linkages are crucial for enhancing overall coordination across the basin. The study finds that: (1) The WEFNR in the Yellow River Basin comprises four dimensions: Cross-Scale Resource Coordination, Systemic Adaptive Dynamics, Institutional Synergy and Governance Depth, Equitable and Functional Eco-Infrastructure. (2) From 2013 to 2022, the WEFNR in the Yellow River Basin exhibited increased volatility, with internal linkages and external interactions becoming more coordinated, and overall risk resistance improving; the spatial pattern featured an “upstream bulge–midstream depression–downstream uplift,” with high resilience values concentrated along the main river course and in core cities. (3) The spatial association network revealed a distinct “core-periphery” structure, with upstream and downstream cities occupying central network positions. Resource-intensive and economically developed cities demonstrated significant spillover effects, yet cross-cluster coordination remained weak and structural barriers persisted. Rising temperatures and industrial structure optimization inhibited network formation, while larger government size and greater innovation capacity promoted stronger inter-city linkages. (4) The basin-wide WEFNR exhibited both absolute and conditional β-convergence; however, innovation capacity suppressed convergence, and government scale also had a dampening effect under networked conditions. Sub-basin analysis revealed significant inhibitory effects of innovation capacity in the midstream and downstream regions, with weak divergence trends observed primarily in central and lower-middle cities, while central cities displayed a positive development trajectory. Based on these findings, this study proposes a coordinated optimization strategy for enhancing WEFNR in the Yellow River Basin, offering new theoretical and practical insights for resilience research in similar global basins.