In this study, the crude exopolysaccharides (CEPSs) from fungus Aspergillus cristatus (MK346334, NCBI) isolated from Fuzhuan brick tea and its main purified fraction (EPSs-2) were investigated. Using the RAW264.7 cell model, EPSs-2 exhibited an excellent immunomodulatory effect in vitro. Then, the regulating effects of EPSs on immune function and gut microbiota were evaluated using a cyclophosphamide (Cy)-induced mice model. It was found that both CEPSs and EPSs-2 improved the body weight loss, immune organ indexes as well as the levels of TNF-α, IL-1β, IFN-γ and IgA, exhibiting potent immunoregulatory activity. Moreover, CEPSs and EPSs-2 not only attenuated the intestinal tissue damage, but also promoted the production of short-chain fatty acids and modulated the microbial composition by increasing the growth of Muribaculaceae, Prevotellaceae_UCG-001, Bacteroides, Parabacteroides and Tidjanibacter, while decreasing the relative abundances of Helicobacter, Bilophila, Mucispirillum, Lachnospiraceae, Ruminococcaceae and Clostridiales. These results indicated that the EPSs, especially EPSs-2, exhibited immunomodulatory activity associated with the modulation of gut microbiota to maintain gut homeostasis, which provided evidence for the development of novel potential prebiotics and immunomodulators.