The mycelium biofloc bioaugmented by Cordyceps strain C058 effectively purifies water, which may be related to the synthesis of extracellular polymer substances. To verify this conjecture, we analyzed the changes in extracellular polymer substances content in the mycelium biofloc under various hydraulic retention times (36 h, 18 h, and 11 h). The microstructure and microflora composition were analyzed using a scanning electron microscope and high-throughput sequencing. The ordinary biofloc without bioaugmentation was taken as a control. The results showed that under the above hydraulic retention time, the extracellular polymer substances contents of the mycelium biofloc were 51.20, 55.89, and 33.84 mg/g, respectively, higher than that of the ordinary biofloc (14.58, 15.72, and 18.19 mg/g). The protein content or the polysaccharide content also followed the same trend. Meanwhile, the sedimentation performance of the mycelium biofloc was better than that of the ordinary biofloc, attributed to the content of the extracellular polymer substances. It is worth noting that C058 is the main biofloc content, which promotes the synthesis of extracellular polymer substances in the mycelium biofloc. Other functional microorganisms in the mycelium biofloc were Janthinobacterium, Phormidium, Leptolyngbya, Hymenobacter, and Spirotrichea, which also promote the synthesis of extracellular polymer substances.