The eastern part of the northern margin of the North China Craton is a key metal metallogenic province in China, hosting many important rare metal and rare earth element (REE) deposits and having great resource potential. This study investigated the Saima deposit, a niobium (Nb) and tantalum (Ta) deposit and the Baerzhe deposit hosting zirconium (Zr), Nb and REEs. Based on previous LA-ICP-MS zircon U–Pb dating results obtained by the authors’ team, this study compared the whole-rock geochemistry and whole-rock Sr–Nd–Pb isotopes of an orebody with its surrounding rocks. The geochemical characteristics of both deposits are used to systematically review the evolution of the alkaline magma and the differences in the physical and chemical conditions for enrichment and mineralisation of late-stage rare elements and REEs such as Nb, Ta and Zr. Comparing the mineralisation of the Saima and Baerzhe deposits, the alkaline magmatic evolution plays a crucial role in the enrichment of rare-earth elements, which are generally formed in the late stage of alkaline magmatic evolution.