Marine sedimentary phosphorites usually contain high rare earth elements (REEs) content, especially the heavy REEs (HREEs), which account for over 30% of the total REEs. The phosphorites may became another important source for HREEs in the future. Phosphorite deposits are widely distributed in China and most of them are found in Yunnan, Guizhou, Sichuan Provinces, etc. High REEs abundances are confirmed in the Zhijin phosphorite deposit in Guizhou Province and with total REEs resource over 3 Mt. The collophanite and apatite are the main host phase for both REEs and P, and the collophanite has complex chemical composition. There are still controversies for the mineral and chemical composition of collophanite. Based on detailed petrological, mineralogical, SEM/EDS, XRD, FIB-TEM and LA-ICP-MS results of phosphorites in Zhijin deposit, this paper discuss the mineral composition of phosphorites and the origin of the complex chemical composition of collophanite. The results show that the most phosphorites in the deposit show the pelletal texture,which is composed of phosphorous pellets and carbonate cement. The mineral composition of the phosphorous pellet is very complex, including mainly fluorapatite and dolomite, and with minor quartz, dolomite, pyrite (some oxidized into limonite), muscovite, solid bitumen and barite. The mineral composition of the cement is mainly dolomite, with minor quartz, pyrite, barite, and trace amounts of zircon, rutile, and liebigite (possibly formed by oxidation of other uranium minerals). The FIB-TEM results show that the cryptocrystalline part of the outer layer of phosphorus pellet is composed of nanoscale mineral aggregates including mainly nanoscale fluorapatite, and small amount of nanoscale dolomite, pyrite and organic matter. The mineral composition of collophanite is similar to that of phosphorus pellet. The discovery of nanoscale fluorapatite, dolomite, pyrite, and organic matter in phosphorite provides reliable evidence for explaining the chemical complexity of collophanite. The discovery of solid bitumen and liebigite in phosphorites, as well as high REEs content in organic matter, also provides new evidence for an alternative occurrence of U and REEs in phosphorites.