The mineralization within the North China Craton (NCC) is intricately linked to Mesozoic large-scale extension in eastern China and is a consequence of a unified geodynamic tectonic background. Despite previous attempts to elucidate the relationship between large-scale mineralization and magmatic activity in the NCC, a lack of systematic research has hindered the identification of connections among deposits with inconsistent metallogenic ages. This study focuses on the coal measures of the Huanghebei Coalfield (HHBC) in western Shandong, presenting a regional magmatic–hydrothermal metallogenic system with a genetic connection. It delves into the intricate interplay between the multi-mineral enrichment mechanism, metallogenic regularity, and the NCC’s destruction. The findings reveal that: (1) Various stages of magmatic intrusion during the Yanshanian period significantly influenced the Late Paleozoic coal measures in the HHBC. The coal measures exhibit distinct ranks, ranging from medium-rank bituminous C to A and high-rank anthracite C, resulting in noticeable differences in gas generation among different coal ranks. The shale between the coal seams C5 and C7 emerges as excellent with a good hydrocarbon-generating capacity during the middle-maturity stage. (2) The “Intrusion along the rock layer type” proves most conducive to shale gas enrichment, while the “laccolith type” is more favorable for shale gas enrichment compared to “dike type” intrusions, which have a limited impact on shale gas enrichment. (3) The mineralization process of CBM, shale gas, and iron ore is influenced by Yanshanian-period magma. The enrichment degree of CBM and shale gas exhibits an inverse correlation with the distance from the magmatic intrusion. Iron deposits demonstrate a close association with the magmatic intrusion, with enhanced enrichment along the rock layer. The results indicate that the destruction of the NCC triggered intense metasomatism in the deep cratonic fluids, serving as the primary driving mechanism for large-scale mineralization during the Yanshanian period. Magmatic intrusions bring hydrothermal fluids conducive to mineralization, and the heat release from these intrusions promotes thermal evolution, hydrocarbon generation, and the enrichment of organic-rich strata.