Rare earth elements (REEs) are important strategic metal resources, and ion-adsorption type heavy rare earth ores are a distinctive resource in China. The Shitouping heavy REE (HREY: Gd-Lu and Y) deposit, recently discovered in southern Jiangxi Province, is a super-large ion-adsorption type HREY-rich deposit. The ore body exhibits differentiated enrichment characteristics with the coexistence of light REE (LREE: La-Eu) and HREY ores, described as “upper LREE and lower HREY”. However, the genetic mechanism of this deposit has not been well constrained to date. Here, an integrated genetic study was conducted on a typical weathering crust profile from the Shitouping deposit using mineralogy, element geochemistry, REE speciation analysis, and pH measurement via techniques including X-ray Diffraction, Electron Probe Microanalysis, X-ray Fluorescence Spectroscopy, Inductively Coupled Plasma Mass Spectrometry, and Sequential Extraction.The results indicate that the underlying syenogranite bedrock is rich in easily weatherable LREE- and HREY-bearing minerals such as bastnäsite and synchysite. Upon weathering and decomposition, these minerals release abundant LREE and HREY ions into the weathering crust, serving as the primary material source for REE mineralization. The bedrock has a total REE content of 558×10-6, with both LREE and HREY being fertile, and HREY is more enriched (LREE: 242×10-6, HREY: 316×10-6, LREE/HREY ratio=0.77; HREY accounts for 56.6%), classifying it as a HREY-rich ore-forming parent rock. From bottom to top in the weathering profile, rock-forming minerals such as feldspar and mica gradually weather and decompose, eventually being replaced by secondary clay minerals dominated by kaolinite and illite, which become the main hosts for adsorbed REE ions. Due to weathering and leaching, REEs migrate within the weathering crust and concentrate in the lower part of the fully weathered layer to form an ion-adsorption type REE ore body. The upper section of the ore body is primarily enriched in LREE, while the lower section is more strongly enriched in HREY, demonstrating a dual-layer enrichment pattern of “upper LREE and lower HREY”.In the studied profile, REEs are present mainly in the ion-exchangeable (F2: (29.8-330)×10-6, accounting for 4.5%-59.0%), Fe-Mn (hydr)oxide (F5: (55.9-318)×10-6, 11.6%-40.8%), and residual (F7: (74.7-197)×10-6, 22.2%-29.8%) fractions. In contrast, only minor amounts of REEs were found in the humic acid-bound (F4: (5.02-86.3)×10-6, 1.49%-11.0%), strongly organic-bound (F6: (23.1-182)×10-6, 9.47%-23.4%), carbonate-bound (F3: (0.11-3.41)×10-6, 0.01%-1.4%), and water-soluble (F1: (0.11-4.26)×10-6, 0.02%-0.55%) fractions. The pH of the weathering crust profile transitions from weakly acidic at the top to weakly alkaline at the bottom, with values ranging from 5.4 to 8.8. Based on our findings, we propose that the “upper LREE and lower HREY” enrichment pattern in the Shitouping deposit is primarily controlled by the REE characteristics of the parent rock and the distinct speciation and migration behaviors of LREEs and HREYs during weathering. Firstly, the parent rock provides ample sources for both LREE and HREY mineralization. Secondly, the ion-exchangeable, Fe-Mn (hydr)oxide, and organic-bound fractions are the dominant, potentially minable phases. Notably, the ion-exchangeable fraction is more enriched in LREEs and is concentrated in the upper part of the profile. In contrast, the Fe-Mn (hydr)oxide and organic-bound fractions show a strong preference for HREY and are more enriched in the middle and lower parts. This differential distribution is a key factor leading to the development of the dual-layer ore body. Furthermore, the genesis of the deposit is also influenced by the properties of clay minerals, pH conditions, redox environment, and groundwater mobility within the weathering crust.