Natrophilite is a rare phosphate mineral that has not been reported in China, especially its primary mineral, which has not been discovered both domestically and internationally. The literature with a few data suggests that natrophilite is formed by sodium replacement of lithiophilite as a secondary mineral. Lithiophilite is a common mineral in pegmatite, which is generally believed to be a product of the magmatic stage in phosphate rich pegmatites as a primary mineral. In this article, natrophilite and lithiophilite developed on natrophilite were found in the Chakabeishan rare-metal pegmatite. Natrophilite is characterized by euhedral mineral particles without any metasomatism, and has primary mineral features of apatite alteration. And the lithiophilite is irregular and develops on the natrophilite, showing typical metasomatic characteristics. Moreover, electron probe data showed that the Mn/Fe values of natrophilite were 1.692-1.875, and the Mn/Fe values of lithiophilite were 2.519-2.548. This also indicates that the formation of natrophilite occurred earlier than that of lithiophilite. Natrophilite should be the primary mineral, and the lithiophilite should be the secondary mineral. The higher manganese content of the parent magma in the pegmatite area may be a possible reason for the occurrence of natrophilite. The alteration of lithiophilite and fluoroapatite developed on the natrophilite reflect the later oxidation and metasomatism of Li, Mn, Ca, and F rich fluids. Meanwhile, combined with the alteration of spodumene in this area, it is indicated that there is a geochemical cycle of lithium in the Chakabeishan deposit.