The aluminum-bearing rock series in southeastern Chongqing occurs above the Huanglong Formation limestone and has undergone a multistage weathering–mineralization evolution from “ore-forming parent rock→ claystone → bauxite rock → bauxite ore.” Based on XRD, XRF, and ICP-MS analyses of drill-core samples, together with weathering indices such as CIA and ICV and mass-balance calculations using Grant’s equation and Isocon diagrams, this study systematically investigated the element migration and enrichment patterns as well as the metallogenic mechanism of the area. The results show that the weathering intensity in the study area was generally extremely high: CIA increased rapidly from the limestone stage and approached 100 in the bauxite stage, indicating intense chemical weathering and sustained leaching during ore formation. Element migration exhibited pronounced stage-specific characteristics. During the lateritization stage, Ca, Sr, and Ba, which are associated with carbonate minerals, were strongly depleted, whereas Al and Si were relatively enriched. During the desilicification and aluminum-enrichment stage, SiO2 was intensively leached, Al2O3 was significantly enriched, and key metals such as Li were concentrated. During the purification and enrichment stage, impurity elements were further removed, Al became relatively purified, and associated elements such as Ga, V, and Cr were enriched. Correlation analysis indicates that Li is mainly controlled by clay minerals, Ga is primarily incorporated into aluminosilicate minerals through isomorphic substitution, and REE are jointly controlled by iron–manganese oxides, clay minerals, and the weathering–diagenetic environment. This study suggests that the bauxite mineralization in southeastern Chongqing is essentially the result of carbonate dissolution, clay formation, desilicification and aluminum enrichment, and diagenetic purification driven by an extreme warm and humid climate, providing geochemical constraints for prospecting and resource evaluation of bauxite and associated critical metals in the region.