Fine-scale characterization of deep structures in ore districts is of great significance for revealing sources of ore-forming materials, characteristics of ore-controlling structures, and deep mineral exploration. Traditional methods such as seismic exploration and electromagnetic surveys are often constrained by field conditions and high costs in complex mining areas, making large-scale, high-resolution imaging difficult to achieve. Ambient noise surface-wave tomography extracts surface-wave dispersion information from ambient noise without the need for active sources, offering advantages such as high imaging efficiency, high lateral resolution, and strong adaptability. In this study, a linear array of 49 stations with an inter-station spacing of 250 meters, covering a total length of 12 km, was deployed in the Zhalageamu ore district in Inner Mongolia. Continuous ambient noise data were recorded for 21 days. Rayleigh wave dispersion curves were extracted through cross-correlation, and the S-wave velocity structure from the surface to a depth of 2 km was obtained via inversion using the one-step surface-wave tomography method. The results reveal significant lateral heterogeneity in the shallow S-wave velocity structure of the study area, with different velocity anomalies accurately delineating the boundaries of strata and rock masses. A shallow dome-like emplacement feature of granodiorite is identified. The ore bodies are predominantly located within the shallow low-velocity anomaly zones, indicating that their occurrence is jointly controlled by intrusive rocks, contact zones, and fault fracture zones. This study not only provides new geophysical constraints on the deep structure and metallogenic mechanisms of the Zhalageamu ore district but also validates the effectiveness and applicability of ambient noise tomography in the exploration of ore districts.