The Weishan REE deposit is one of the largest LREE deposits in China, which is hosted by the Weishan alkaline complex (WSAC) and late Archean gneisses. Two types of mineralization including vein-type and disseminated-type occur in this deposit, of which the former is characterized by large quartz-sulfate-calcite-REE mineral veins cutting all kinds of wallrocks, while the latter is featured by REE minerals disseminated in the alkaline rocks. The vein-type mineralization commonly occurs at shallow depths and has been numerously studied. The disseminated-type mineralization typically occurs at deeper depths, which was newly discovered by drilling exploration and has been poorly studied. In this contribution, zircon U-Pb dating and Hf isotopic analysis as well as whole-rock geochemistry and Sr-Nd isotopic analyses were conducted on the deeply drilled alkaline rocks, combined with molybdenite Re–Os dating on the disseminated ore, with the aim to unravel the petrogenesis of the alkaline rocks and their contributions to the REE mineralization. Zircon U–Pb dating suggests an intrusive age of 119.9 ± 0.9 Ma for the WSAC, which is quite consistent the Re–Os age of 120.0 ± 1.8 Ma for the disseminated ore, corroborating their close genetic correlation. The studied alkaline rocks show enrichment of LILEs, depletion of HFSEs and strong fractionation between LREEs and HREEs, indicating a crustal involvement in the magmas or a metasomatized mantle source. They are characterized by higher Hf (εHf(t) = -6.7 to −12.2) and Nd (εNd(t) = -8.8 to −9.7) isotopic compositions compared with those of the contemporaneous subcontinental lithospheric mantle (SCLM). Based on the above features, it is inferred that the parental magmas of the WSAC were mainly derived from an enriched SCLM with some involvement of asthenospheric mantle-derived materials. The mantle source was likely metasomatized by the subducted Paleo-Pacific oceanic plate, leading to the enrichment of REE and carbonate. Rollback of the oceanic slab during the early Cretaceous resulted in an extensional setting in the study region, which was favorable for partial melting of the metasomatized mantle and thus generated the REE-rich alkaline magmas.