Alginic acid, which is widely used in various industries like food, cosmetics, biomedical, and pharmaceuticals, is an unbranched polysaccharide derived from matrix and cell walls of brown algae. It has a backbone of 1, 4-glycosidic bonds with two conformational residues arranged randomly, β-D-mannuronic acid (M) and α-L-guluronic acid (G). Recently, alginic acid has been found to exhibit physiological activities such as anti-inflammatory, antioxidant, and cholesterol lowering, drawing attention again as a functional biomaterial. However, there are still few studies on the relationship between the structural characteristics of alginic acid and the biological function. This is because, unlike other polysaccharides, alginic acid does not have a repeating unit and has a heterogeneous structure. Here, we have developed an analytical strategy for characterization of alginic acid using LC/MS/MS. To facilitate the structural analysis, alginic acid was acid hydrolyzed to small oligomers, which are further purified by PGC-SPE. The acid-hydrolyzed alginic acid was chromatographically separated on a PGC column suitable for isomer separation and analyzed by MS/MS. This analytical strategy enabled us to obtain M/G ratio, degree of polymerization, molecular weight, modification, impurities, and quantitative information. In addition, comparative analysis was performed on various alginic acid products to characterize the structure of alginic acid for each product. Ultimately, it can be used for quality index data of raw materials for the production of high value-added alginic acid products derived from seaweeds by examining the correlation between the structural characteristics and biological functions of alginic acid.