Natural hydrogen is regarded as a potential resource for the global energy transition, and its accumulation is closely linked to water–rock reactions involving Fe²⁺ bearing minerals and effective sealing conditions. The Liaohe Basin, located on the northeastern margin of the North China Craton within a key metallogenic belt, is surrounded by sedimentary-metamorphic iron deposits and is a potential area for natural hydrogen accumulation. In this study, aeromagnetic and satellite gravity data were integrated to estimate basement depth through gravity interface inversion, followed by three-dimensional magnetic susceptibility and density inversion and structural–mineralization correlation analysis. The results reveal strong basement heterogeneity. Iron-rich anomalous bodies show clustered and belt-like to dome-like distributions, mainly along the transitional zone between deep depressions and basement uplifts. Combined density–magnetic zonation suggests that high-density, high-magnetic units may correspond to iron-rich bodies, whereas high-magnetic, low-density units likely indicate fractured and altered fluid pathways. Based on the measured results of surface hydrogen concentration, it is inferred that the high magnetic anomaly in the uplift transition zone at the edge of the depression might be the coupling area of iron-rich rock bodies and channel zones, which is the priority response area of natural hydrogen in the Liaohe Basin, China.