Doenjang and Ganjang are the most consumed fermented soybean foods in Korea. One of the important ingredients for making these foods is Meju. The nutritional and organoleptic quality of the traditional Meju is highly related with its bacterial and fungal community profiles. Various microorganisms hydrolyze and modify soybean macromolecules, yielding smaller functional and flavoring compounds. Carbohydrates can be hydrolyzed and transformed by the microorganisms as well, generating various oligosaccharides and monosaccharides. In this study, in order to elucidate the role of individual microorganisms in the utilization of carbohydrates, the oligosaccharide and microbial community changes during fermentation were analyzed using HPLC Q-ToF MS and amplicon-based NGS methods. Total 19 oligosaccharide compositions were found in Meju. Among them, hexose containing oligosaccharides such as raffinose and stachyose, are degraded during Meju fermentation; however, their isomeric oligosaccharides and several HexNAc-containing oligosaccharides are newly synthesized. Correlation analysis suggested the relationship between microbial communities and oligosaccharide profiles. Enhydrobacter showed negative correlation with (Hex)₃, (Hex)₄, and (Hex)₅ oligosahaccharides, and (Hex)₆ and (Hex)₇ oligosaccharides had a positive correlation with Leuconostoc.