Pyrodextrin (PD) is prepared from starch by heat treatment and is resistant to amylase. We hypothesized that PD might have prebiotic potential affecting the microbiota composition, because it contains a non-digestible portion that may behave as dietary fiber. This study investigated the effects of PD supplementation on growth performance, gut morphology, short-chain fatty acids (SCFAs), and the bacterial community in weaned piglets receiving dietary supplementation of 0.5% PD. The piglets in the PD (treated) groups showed greater antioxidant capacity and feed efficiency (P < 0.05), as well as improved intestinal morphology in comparison with the piglets in the weaned (control) group. Gut microbiota profiles were assessed through 16S rRNA sequencing on the ileum contents and feces of early weaned piglets. Several genus-level enrichments and depletions were observed in response to PD treatment. Of note, PD supplementation decreased the relative abundance of pathogenic organisms, including Defluviicoccus and Gardnerella, while markedly increasing that of commensal bacteria (genera Psychrobacter and Prevotella), which have important roles in nutrient absorption and immune response regulation. The most notable effect in the PD treatment groups was increased production of SCFAs in the feces of PD-treated weaned piglets. Correlation analysis revealed that the improvement in SCFAs was positively correlated with the increase in SCFA-producing bacteria. Overall, this study provides a more comprehensive understanding of the effects of PD supplementation on the fecal microbial community and the modulation of SCFA production in early weaned piglets, thus indicating that PD can be used to alleviate weaning stress in piglets.