Increasing evidence has shown that the gut microbiota plays an important role in preventing obesity; however, the mechanism by which insoluble dietary fiber (IDF) prevents high-fat diet (HFD)-induced obesity remains unclear. This study aimed to investigate the effect of SIDF on obesity in HFD mice and determine the mechanism by which it prevents obesity through regulating the gut microbiota. Soybean insoluble dietary fiber (SIDF) was used as an intervention in HFD mice for 20 weeks. The results showed that SIDF significantly reduced the body weight (BW), fat index, total cholesterol, triglyceride, and low-density lipoprotein cholesterol while increasing the content of high-density lipoprotein cholesterol in HFD mice. SIDF intervention was also beneficial for the reduction of liver lipid content and fatty droplets in mice. Furthermore, SIDF intervention improved the gut microbiota composition by increasing the relative abundance of potentially beneficial bacteria (such as Lactobacillales [order], Lactobacillus [genus], Lachnospirace_Nk4A136_group [genus]), and reduced the relative abundance of potentially harmful bacteria (such as Lachnospiraceae [family] and Bacteroides_acidifaciens [species]), which correlated with obesity (at least p < 0.05 in all instances). Finally, SIDF was fermented by related beneficial bacteria, which increased the content of the short-chain fatty acids (SCFAs), and promoted the secretion of satiety hormones. In conclusion, SIDF intervention could prevent obesity in HFD mice by modulating the gut microbiota composition. Hence, SIDF may be used as a potential ingredient in functional foods.