Here we report the relationships between magnetic anomalies and polymetallic mineralization established by analysis of ground magnetic data for the Southern Great Xing'an Range (SGXR), Northern China. We present magnetic anomaly features, identify fault structures (including regional NE–SW- and NW–SE-striking conjugate faults and near-E–W-striking fault systems), and determine the spatial distribution of intrusive magmatic rocks with high magnetic susceptibility in the range. We demonstrate the influence of magmatic intrusions on polymetallic mineralization by spatial comparison of these features with the known geology and inferred structures. We conclude that the main polymetallic deposits in the SGXR are located in zones with steep-gradient variations in magnetic anomalies at the contacts between host strata and intrusive magmatic rocks. We delimit several prospective areas of polymetallic deposits in the study area. The findings should guide further exploration of polymetallic deposits and deep subsurface prospecting in the SGXR.