This study was conducted to the determine fermentation characteristics of soybean oligosaccharides (SBOS) in an in vitro system. Digesta collected from the colon of Huanjiang mini-pigs was used as inoculums, and SBOS (0.2 g per 10 mL fermentation broth) was used as substrate during the in vitro fermentation. The inoculum or inoculum + glucose (0.2 g) was used as negative or positive control, respectively. The slurry was fermented in an anaerobic chamber and gas production (GP) recording was taken after 48 h of incubation by referring to the moving scale on the plunger of the glass syringes, and then GP parameters, pH value, NH(3)-N content, short chain fatty acid (SCFA) levels, and microbial community in the fermentation broth were determined. For gas production parameters, pH, and fermentation product determination after 1, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 28, 32, 36, 42, and 48 h of incubation, SBOS and glucose demonstrated similar responses compared to control including increase maximal gas production, decreased lag time, decreased pH, and accumulation of NH(3) and increased SCFA. The exception was rate of GP, which was higher (P < 0.05) for SBOS compared with glucose. Incubation with SBOS increased (P < 0.05) the microbial diversity and population of Bifidobacterium and Lactobacillus but decreased (P < 0.05) Escherichia and Streptococcus when compared with incubation with glucose. These findings suggested that the SBOS can improve the gut microbiota balance in colon and modulate its metabolism.