The Ediacaran sediments in the Yangtze Block preserve valuable records of biological evolution and drastic climate changes. However, most of the Ediacaran fossil occurrences have been reported from the shallow platformal facies, and few fossils have been described from the deep basinal facies in the Yangtze Block. Here, we report mineralized microfossils from the basinal facies of the Ediacaran Doushantuo Formation at Fengtan in northwestern Hunan Province, China. The submillimeter-sized microfossils with oval-discoidal shapes have apatite walls of variable thickness. The lack of morphological regularity, ornamentation, and distinct apertures indicates that they are not protozoan shells or tests. The apatite walls have more likely replaced the recalcitrant organic walls of prasinophyte phycomata and/or algal resting cysts. These fell from shallow water and were quickly preserved in a deeper setting, associated with a local decline in pH caused by bacterial decomposition and elevated concentration of phosphate in seawater. This discovery provides new insight into the stratigraphic correlation between the shallow and basinal facies of the Chinese Ediacaran.