A set of microbial reef is developed in the Honghuayuan Formation at the Huanghuachang section in the Yichang, Hubei Province. The microbial reef contains well-preserved thrombolites, one of the important types of microbial carbonate (i. e. thrombolite) . Based on the previous studies on the reef-building role of the metazoan and metazoan communities in Early Ordovician reefs in South China, this paper mainly studied the formation mechanism of thrombolite in microbial reefs by combining the macroscopic and microscopic characteristics of microbial reef through fieldwork and sampling and indoor mill observation. The results showed that the microbial reefs of the Honghuayuan Formation in the Huanghuachang section are dominated by thrombolite, accompanied by a small number of metazoan fossils, such as Calathium , lithistid sponge, bryozoan, etc. This reef represents a special type of microbial reefs in the Early Ordovician, that is, the microbial reefs are dominated by microbial carbonate, and locally metazoan is involved in the reef formation which is a special type of reef in the transition process from microbial reefs to metazoan reefs. At the same time, a large number of calcified cyanobacterial fossils are found in the thrombolite, such as Gerwanella, Subtifloria and Nuia, and the more intuitive calcified cyanobacteria showed that the thrombolites are the products of sedimentation, aggregation and early petrification of biofilm or mats dominated by cyanobacteria, indicating that there was a very close relationship between thrombolite and the complex calcification of microbial mats dominated by cyanobacteria. This study provides a typical example for the study of the formation mechanism of thrombolite in the Early Ordovician microbial reefs in South China and the transition period from microbial reefs to metazoan reefs.