Abstract The Benxi area in Liaoning Province is one of the most important iron-ore districts in China. This study uses nonseismic geophysical data (in the form of gravity–magnetic–magnetotelluric data) and based on the section modeling method to model the deep, three-dimensional geological structure of the Benxi area. Based on the modeling results and deep geological structure characteristics, the Benxi area can be divided into three first-order deep geological tectonic units. A close relationship is between tectonic unit and iron-ore concentrations. First, high-quality iron-ore deposits occur within the tectonic boundary and sedimentary boundary zone of the Jiao–Liao–Ji Belt, reflects the protective effect of sedimentary cover on the iron-bearing formation. Second, enriched iron-ore deposits are mainly developed in Mesozoic granitic intrusion zone, reflects the hydrothermal leaching of silicon in host iron-bearing formations during magma intrusion. Thus, the findings of this study have important implications for future prospecting in the Benxi iron-ore district.