To reveal the functional properties of hazelnut dietary fibers (DFs) in different colonic segments (cecum, proximal, and distal colon), a diet enriched with natural hazelnut, roasted hazelnut, or hazelnut skin DFs was applied to mice for 6 weeks; microbial metabolites, microbial composition, and tissue morphology were determined segmentally using gas chromatography, 16S rRNA sequencing technology, and microscopy, respectively. Roasted hazelnut DFs revealed significantly (p < 0.05) higher propionate in the cecum of female mice, while hazelnut skin DFs significantly increased the butyrate level in the distal colon of male counterparts. 16S rRNA sequencing revealed hazelnut DFs promoted the Lactobacillus animalis, L. gasseri, and Akkermansia muciniphila related OTUs, especially in the proximal colon, but the degrees of promotions were hazelnut type-, segment- and sex-dependent. Interestingly, hazelnut skin DFs significantly (p < 0.05) stimulated Prevotella related OTUs in the distal colon regardless of sex, which is known to have great ability to utilize dietary polysaccharides. Furthermore, hazelnut skin DF group had higher crypt height values, suggesting that hazelnut skin DFs have ability to maintain saccharolytic activity in more distal region of the colon. Overall, our results demonstrate that hazelnut DFs differentially impact microbial metabolite formation, microbiota composition and tissue morphology in different segments of the colon.