Mass alkaline magmatic activities in Western Shandong during the late Mesozoic controlled the mineralization processes of gold and rare earth element (REE) polymetallic deposits in the region. The Chishan alkaline complex is closely associated with the mineralization of the Chishan REE deposit, which, as the third largest light REE deposit in China following the Baiyenebo (Inner Mongolia) and Mianning (Sichuan) deposits, is considered a typical example of alkaline rock mineralization throughout the North China Craton. To determine how the Chishan alkaline complex and REE deposit interact with each other, a systematic study was conducted on the petrology, rock geochemistry, zircon U–Pb geochronology, Lu–Hf isotopes of the quartz syenite, and alkali granite contained in the Chishan alkaline complex. The results reveal that the deposits feature similar geochemical characteristics typical of an alkaline rock series—both are rich in alkali, high in potassium, metaluminous, and poor in Ti, Fe, Mg, and Mn. In terms of REEs, the deposits are strongly rich in light REEs but poor in heavy REEs, with weak negative Eu anomalies. In terms of trace elements, they are rich in large ion lithophile elements Ba, Sr, and Rb but poor in high field-strength elements Nb, Ta, and Hf. Zircon LA-ICP-MS U–Pb dating indicated that the quartz syenite and alkali granite formed in Early Cretaceous at 125.8 ± 1.2 Ma and 127.3 ± 1.0 Ma, respectively; their εHf(t) values are −22.67 to −13.19, with depleted model ages (TDM) ranging from 1296 Ma to 1675 Ma and crustal model ages (TDMC) of 2036–2617 Ma. The Chishan alkaline complex originated from partial of the EM I-type (enriched mantle I) lithospheric mantle with assimilation of ancient crustal materials. The complex is of the same origin as the REE deposit, and developed in an extensional setting that resulted from plate subduction and lithospheric thinning and upwelling in the eastern area of the North China Craton.