Golden-flower fungus, the only dominant microorganism determining the Fu-brick tea quality through fermentation and the important microbe in Liupao tea, is considered a potential probiotic fungus based on its anti-obesity effect. However, the classification of golden-flower fungi is still controversial; the anti-obesity effect of golden-flower fungus polysaccharides remains unknown. In this study, we identify a golden-flower strain as Aspergillus cristatus based on morphological characteristics and multigene phylogeny analysis, which resolves the controversy of classification. Moreover, we find A. cristatus polysaccharides (ACPS) attenuate obesity in rats. ACPS modulate gut bacterial composition, in which Akkermansia, Akkermansia muciniphila, Bacteroides, Romboutsia, Blautia, and Desulfovibrio are considered the core microbes regulated by ACPS. ACPS increase fecal total short-chain fatty acid content and serum, hepatic, and fecal total bile acid content. Furthermore, ACPS-induced gut microbiota alteration plays a causal role in the protection from obesity, according to a fecal transplantation experiment. Thus, ACPS ameliorate obesity by regulating gut microbiota and gut microbiota-related metabolites.