Over the past few decades, numerous ion adsorption type rare earth element (REE) deposits have been discovered in the weathering crusts of granitic and volcanic rocks, and a great deal of studies have been conducted on their characteristics and genesis. Recently, ion adsorption type REE deposits in the weathering crusts of metamorphic rocks were discovered for the first time in Ningdu County, China. Unlike the extensively studied weathering crusts of granitic rocks, the geochemical and mineralogical characteristics of the weathering crusts of metamorphic rocks and the mobility of REEs during weathering processes remain unclear. Our research shows that the bedrocks in the Ningdu area are primarily metamorphic sandstone that contain ~ 200 ppm of total REEs. REEs in the metamorphic rocks are primarily hosted in hydrothermal REE-epidote and rhabdophane-(Ce), implying that hydrothermal fluids, which might have introduced REEs and provided the materials for REE mineralization, are likely one of the most critical factors for mineralization in the weathering crusts of metamorphic rocks. The weathered products of fine-grained metamorphic bedrocks are significantly less permeable than those of granitic rocks; consequently, the weathering crusts are rather thin, usually less than 20 m. The degree of weathering is relatively low, with chemical index of alteration (CIA) values of less than 80. Clay minerals consist primarily of illite, kaolinite, and hydrobiotite. The low permeability of the weathered products causes a short migration distance for water medium carrying REE ions, and the ore bodies in the weathering crusts of metamorphic rocks are primarily located in the middle and upper parts of the completely weathered horizon. Average REE concentrations in the ore bodies are ~ 1000 ppm, of which 70%–80% are ion-exchangeable. The REE distribution patterns of the weathering crusts are largely similar to that of the bedrocks, except for the strong negative Ce anomalies in the topsoils that are caused by the pre-existing positive Ce anomaly layer above the ore body that is thin and removed due to weathering and erosion. Our research results deepen the understanding of the genesis of ion adsorption type REE deposits in the weathering crusts of metamorphic rocks and indicate that the hydrothermal process is the key mineralization factor.