Generally speaking, magmatic-hydrothermal deposits are not only related to intrusions but also closely related to strata and structures. The ore-controlling factors are often complex, and recognition of the most important factor is often critical for a successful metallogenic prediction. Being part of the Dapingtianshan magmatic-hydrothermal metallogenic system, the Shenkuanggou Ag-Pb-Zn deposit in Guangxi is located in the southwestern part of the Longshan nose-like structure in the Southwest of the Dayaoshan uplift. The ores of the deposit are mainly strata-like skarn-type and minor vein-type. Systematic field surveys and research show that the vein-type ores are simple in shape and mainly controlled by the nearly vertical NNW-trending fault. The layered skarn-type ores are very complex in shape, controlled by the Dapingtianshan and Longtoushan plutons and the limestone intercalation in the Cambrian Huangdongkou Formation, the Caledonian complex folding, and the NNW-trending faults as well. The Dapingtianshan and Longtoushan plutons provided ore-forming materials, ore-forming fluids, and heat sources for the formation of the deposit, and controlled the spatial zoning of the ore-forming elements. Limestone intercalation in the Cambrian Huangdongkou Formation is an indispensable material condition for the formation of the skarn-type orebodies, which controls the number and thickness of the ore beds. The EW-trending and NNW-trending composite folds control the specific shape and occurrence of the ore bodies. Faults control the plane space position of the ore block. Based on the understanding of the above ore controlling factors, such as intrusion, stratigraphic lithology, fold, and fault, this paper determines that the NNW-trending fault is the main fluid channel. The Cambrian Huangdongkou Formation limestone interlayer can form a layered skarn-type ore body. Based on this, three ore sections are divided from East to West. A new section was successfully discovered in the West of the mine. This metallogenic prediction has changed the previous fixed mindset, through tracing the nearly EW-trending limestone to trace the layered ore body along the NNW-trending fault (joint). This understanding and experience can be used for reference in the metallogenic prediction of magmatic-hydrothermal deposits controlled by multiple factors in complex fold areas. © 2022 Science Press. All rights reserved.