This paper is the result of mineral exploration engineering. Objective The Manono–Kitotolo spodumene (40%-70%) pegmatite, one of the lithium-cesium-tantalum pegmatite (LCT) in the world, is located at the Mesoproterozoic Kibaran rare metals metallogenic belt in the Democratic Republic of Congo (DRC). The field works revealed that the symbiotic minerals of pegmatite gradually evolved from outside to inside: granite aplite zone(Ⅰ), muscovite-feldspar quartz zone (Ⅱ), quartz albitite zone (Ⅲ), spodumene zone (Ⅳ) and quartz kernel (Ⅴ). Methods In this study, the composition of major elements of mica, spodumene, cassiterite and columbite-tantalite are analyzed by Electron probe X-ray micro-analyzer (EPMA) to bring light on Li-Nb-Ta-Sn mineralization and pegmatitic crystallization differentiation. Results The results show that the content of Rb, Li, and F in muscovite gradually increased from outward (Ⅰ) to inward (Ⅴ), meanwhile the K/Rb gradually decreased. The content of Fe and Rb in lepidolite (V-1) is relatively higher than in muscovite(Ⅱ), which indicating highly fractionated pegmatite inside. Li mineralization mainly occurs in spodumene pegmatite (Ⅳ). Conclusions The grain size of spodumene varies from macro-crystal to coarse grain and medium grain and its principal components keep consistent except Li lost by oxidative leaching, argillation, greisenization and other alterations. Cassiterite with high Nb and Ta is generally formed by greisenization in zone Ⅲ–Ⅳ. Nb-Ta is mineralized in the form of the columbite-tantalite-manganotantalite isomorphism in the zone Ⅱ–Ⅳ, with the development of differentiation, the content of Ta and Mn in minerals increases, while the content of Nb, Fe and Ti decreases and formed Ta-rich and Mn-rich Columbite-tantalite.