Accurate dating of the pegmatite is a challenge due to the uncertainty and controversy of crystallization temperature, fractionation model, and cooling mechanism. In this study, the sizable Nanping No.31 pegmatite vein (southeast China) contain five structural zones that is considered as an ideal example for assessing credible dating method on rare metals pegmatite deposit. The CMS (Chemical composition-Mineral assemblage-Structural geology) classification is applied on the Nanping pegmatite. The No. 31 vein is identified as pegmatite by CMS features. New U–Pb dating CGMs (columbite-tantalite group minerals) in five zones have a consistent age (380 ± 10 Ma). Whilst U–Pb dating of apatite and cassiterite from different structural zones show remarkable two group isotopic ages (370–390 Ma and 145–160 Ma). The much younger age indicated the pegmatite vein has experienced a severe Yanshanian tectono-thermal event at Eastern China. By comparison with apatite, cassiterite and zircon, CGMs is the most suitable mineral for accurate dating of the pegmatite because the dating results of the minerals are much stable, even having metamictization caused by high U content or overprinting by late hydrothermal activity. This study provided new insight into the dating methods for rare metals pegmatites to accurate restrict its metallogenetic geodynamical setting.