The identification of the microstructure and shell composition of small shelly fossils are of great significance for revealing the evolution of the Early Cambrian small shelly fossils, and a large number of small shelly fossils have been preserved in the Early Cambrian Meishucunian Ages phosphorite rock in central Guizhou, but there were few studies on the microstructure and composition of small shelly fossils in the past. In this paper, the microstructure and shell composition characteristics of small shelly fossils in the Cambrian Meishucunian Ages phosphorite rock from Zhijin Xiongjiachang and Qingzhen Luohang in Guizhou Province were analyzed by electron microscope and scanning electron microscope (SEM- EDS) to observe and test individual small shelly fossils in rock thin sections and acid- treated small shelly fossils. The results showed that the diversity of small shell fossils and their shell composition in the phosphorite rock of Zhijin and Qingzhen were consistent, mainly Hyolitha, and their components were fluoroapatite elements such as P, Ca, F, and O. The small shelly fossils preserves obvious nano- scale apatite mineralized particle skeleton, multi- circle structure, dissolved pores and tube nesting. In addition, the in situ micro- element surface scanning of thesmall shelly fossils was carried out by electron exploration, and it was found that the main elements P and Ca were distributed in the small shelly fossils and their fragments, and the cementation almost did not contain P elements. It is comprehensively concluded that most of small shelly fossils in the Cambrian Meishucunian Ages phosphorite rock were buried and preserved in different places, and the later phosphorylation and transport sedimentation of diagenesis in this process had a certain impact on the microstructure and shell composition of the small shell fossils. At the same time, the content of small shelly fossils (including fossil fragments) in the whole rock was inferred by the help of thin- slice full- glass surface scanning, which was positively correlated with the phosphorus content in the phosphorite rock, and it was believed that the prosperity of small shelly fossils in the Cambrian Meishucunian Age had an important contribution to the formation of phosphorite rock in the same period.