Abstract: To investigate the effect of carbon source on microbial diversity in bulking sludge, two different carbon sources, starch and sodium acetate, were used for artificial wastewater and the filamentous sludge bulking was successfully induced. Results show that although different types of carbon sources may cause different SVI, the overall treatment effect of pollutants has not been affected. The occurrence of bulking can not only lead to the decrease of microbial abundance, homogeneity, diversity and richness, but also cause different changes in the relative abundance of microbial community of different categories and functions. Proteobacteria is the phyla with the largest relative abundance in all the sludge samples, and the wastewater environment with starch as carbon source is more conducive to the growth of it. In different microbial communities, the two carbon sources have the greatest influence on the relative abundance of phosphorus removal bacteria. The relative abundance of Thiothrix and Haliscomenobacter, as dominant filamentous bacteria, increases with the sludge bulking under the two carbon sources, while Tetrasphaera is the opposite. The relative abundance of five denitrifier genera represented by Nitrosomonas increases with the sludge bulking, while the relative abundance of seven denitrifier genera represented by Nitrospira and five phosphorus removal bacteria represented by Candidatus Acumulibacter and Candidatus Competibacter decreases. In addition, sludge bulking caused by starch reduces the number of OTUs in the reactor by 251, more than 5 times that of acetate, indicating a greater impact on microbial diversity.