The glycosylation reaction, which is key for the studies on glycoscience, is challenging due to its complexity and intrinsic side reactions. Thioglycoside is one of the most widely used glycosyl donors in the synthesis of complex oligosaccharides. However, one of the challenges is its side reactions, which lower its yield and limits its efficiency, thereby requiring considerable effort in the optimization process. Herein, we reported a multifaceted experimental approach that reveals the behaviors of side reactions, such as the intermolecular thioaglycon transformation and N-glycosyl succinimides, via the glycosyl intermediate. Our mechanistic proposal was supported by low temperature NMR studies that can further be mapped by utilizing relative reactivity values. Accordingly, we also presented our findings to suppress the generation of side products in solving this particular problem for achieving high-yield glycosylation reactions.