As a by-product of juice industry, blueberry pomace is still a rich source of phytochemicals with potential benefits for human health. However, studies about blueberry pomace utilization are insufficient. In this study, the blueberry pomace was fermented by the probiotic Lactobacillus casei and the potential function of fermented blueberry pomace (FBP) was evaluated, including the antioxidant activity, the regulation of fecal microbiota and the production of short chain fatty acids (SCFA). The results showed that FBP obtained improved antioxidant activity which was positively correlated with the content of polyphenols. The microbiota community structure was improved by FBP through inhibiting Escherichia coli, Enterococcus and the ratio of Firmicutes and Bacteroidetes as well as improving Bifidobacterium, Ruminococcus, Lactobacillus, Akkermansia and butyrate-producing bacteria. The SCFA, especially acetic, butyric and lactic acids, were remarkably increased because of FBP-supplementation. Further, UPLC-MS analysis showed that forty-six phenolic compounds were detected in FBP while only thirty-eight in non-fermented blueberry pomace (NFBP), explaining the speculation of this study that the phytochemicals in FBP might increase the gut-improving function. This study suggested that the Lactobacillus casei-fermentation was useful for utilizing blueberry pomace as a potential candidate for functional foods.