Indigestible glucans (IGs) are dietary fibers that can promote human health via fermentation by the gut microbiota, where their physico-chemical properties play a crucial role. This effect remains to be fully explored. The aim of the current study was to comprehensively investigate and compare the fermentation characteristics of IGs with various structural properties, as well as their effects on the gut microbiota. Barley β-glucan (BG), laminarin (L), yeast β-glucan (BY), pachyman (PAC), resistant starch (R), and litesse (Lit) were anaerobically batch-fermented using the human fecal microbiota for 48 h. All the IGs were utilized by the gut microbiota at different rates, and 2% of L, 14% of BG, 23% of BY and PAC, and 35% of R and Lit were unfermented at the 48th hour. During fermentation, mono-, di-, or trisaccharides were released from BG, L, and Lit, and the pH of broth was greatly lowered by IGs, especially BG and L, along with the production of short-chain fatty acids. Interestingly, PAC favored butyric acid production, while BG, L, and BY preferred propionic acid. Moreover, lactic acid, but not succinic acid, was detected in considerable amounts, but only with BG and L after 5 h. 16S rDNA analysis showed different microbial structures and the selective promotion of bacteria with different IGs, while only PAC did not decrease microbial α-diversity. Further qPCR analysis confirmed that BG was more potent at proliferating Faecalibacterium prausnitzii; BY preferred total bacteria, Prevotella, and Lactobacillus; and R favored Bifidobacterium. The IG-induced changes in the gut microbiota were strongly correlated with carboxylic acid production. In conclusion, the six IGs differed in fermentation characteristics and gut microbiota regulation capacity, and each one could have specific applications in human health promotion.