Resistant starches (RSs) with different structural features were isolated from both native and pullulanase-debranched and acid-hydrolyzed pea starches. Their microscopic changes, short-chain fatty acids (SCFA) composition, microbiota communities, and structural characteristics of the corresponding fermenta residues by the end of 24 h of the in vitro fermentation period were investigated. The microbial fermentation clearly caused numerous cracks and erosion on the RS granule surface. In comparison to the positive control, significantly higher levels of butyrate, propionate, and total SCFA were produced after 24 h of in vitro fecal fermentation when resistant starches were used as substrates. The RS substrates with different structural characteristics enabled varying growth of spp., spp., and spp. The discrepancy in microbiota communities associated with the differences in SCFA from the fermentation of RS with different structural features would be critical toward the rational design of foods containing resistant starch with targeted health benefits.