This study sought to investigate any additive or interactive effects that soy isoflavones may have on the ecosystem of the gut, which is influenced by fructooligosaccharide (FOS) in colon-cancer model rats. Male Sprague-Dawley rats treated with 1,2-dimethylhydrazine were given experimental diets containing 0, 3, 6, or 9% FOS with or without 0.1% soy isoflavone for 12 weeks. In addition to the effects of FOS dosage on the gut ecosystem, dietary supplementation with soy isoflavone reduced the number of colonic aberrant crypts (ACs). The fecal weight, fecal pH, and gut transit time significantly decreased in a dose-dependent manner in rats fed FOS and the fecal concentration of bifidobacteria was higher in rats fed FOS than in control rats. The fecal output of total short-chain fatty acids, acetate, and propionate was significantly increased by the presence of FOS and was negatively correlated with the number of ACs, whereas the fecal output of butyrate showed no significant correlation with FOS dosage. The addition of soy isoflavone to the diet did not result in any significant differences in gut ecosystem parameters. Therefore, we conclude that the suppressive effect of soy isoflavone on ACs was not associated with the intestinal ecosystem, which was significantly altered by the dosage of FOS.