The anomalous enrichment of the rare earth elements and yttrium (REY), U, Mo, As, Se, and V in the coal-bearing intervals intercalated within the carbonate successions in South China has attracted much attention due to the highly promising recovery potential for these elements. This study investigates the mineralogical and geochemical characteristics of the late Permian coal-bearing intervals (layers A–F) intercalated in marine carbonate strata in the Xian’an Coalfield in Guangxi Province to elucidate the mode of occurrence and enrichment process of highly elevated elements. There are two mineralogical assemblages, including quartz-albite-kaolinite-carbonates assemblage in layers D–F and quartz-illite-kaolinite-carbonates assemblage in layers A–C. Compared to the upper continental crust composition (UCC), the REY, U, Mo, As, Se, and V are predominantly enriched in layers A and B, of which layer A displays the REY–V–Se–As assemblage while layer B shows the Mo–U–V assemblage. The elevated REY contents in layer B are primarily hosted by clay minerals, zircon, and monazite; Mo, U, and V show organic association; and As and Se primarily display Fe-sulfide association. Three geological factors are most likely responsible for geochemical anomaly: (1) the more intensive seawater invasion gives rise to higher sulfur, Co, Ni, As, and Se contents, as well as higher Sr/Ba ratio in layers A–C than in layers D–F; (2) both the input of alkaline pyroclastic materials and the solution/rock interaction jointly govern the anomalous enrichment of REY; and (3) the influx of syngenetic or early diagenetic hydrothermal fluids is the predominant source of U, Mo, V, Se, and As.