This study investigated the impact of a transglycosylated product (ACOD) catalyzed by Leuconostoc mesenteroides MKSR dextransucrase using sucrose as a glucosyl donor and both maltose and Artemisia capillaris as acceptors on gut microbiota through fecal fermentation. ACOD promoted the growth of probiotics such as Lactiplantibacillus plantarum, Lacticaseibacillus casei, Lacticaseibacillus rhamnosus GG, and Leuconostoc mesenteroides MKSR, while inhibiting the growth of pathogenic bacteria such as Escherichia coli, E. coli O157:H7, Enterococcus faecalis, Listeria monocytogenes, Staphylococcus aureus, Shigella flexneri, Streptococcus mutans, Pseudomonas aeruginosa, and Bacillus cereus during independent cultivation. Fecal fermentation for 24 h revealed that ACOD significantly increased the production of short-chain fatty acids (SCFAs) compared to the blank and fructoooligosaccharide (FOS) groups. Specifically, ACOD led to a 4.5-fold increase in acetic acid production compared to FOSs and a 3.3-fold increase in propionic acid production. Both the ACOD and FOS groups exhibited higher levels of butyric acid than the blank. Notably, ACOD significantly modulated the composition of the gut microbiota by increasing the relative abundances of Lactobacillus and decreasing Escherichia/Shigella and Salmonella. In contrast, FOSs remarkably promoted the growth of Salmonella. These findings suggest that ACOD is a potential candidate for prebiotics that improve the intestinal environment by being actively used by beneficial bacteria.