Polyethyleneglycol diglycidyl ether (PEGDE) is a new generation of cross-linker with the advantages of low toxicity and improved elasticity. The physicochemical properties of PEGDE-HA are closely related to its degree of modification (MoD), effective cross-linker ratio (CrR), as well as modification types/positions. In this study, we developed a structural analysis method for comprehensive characterization of PEGDE cross-linked HA. Combined HPLC-MS/MS analysis accurately measures the parameters of MoD and CrR, and ambiguously locates modification sites/residues. Using the established method, we have, for the first time, identified the existence of intrachain cross-linked structures in the hydrogel and revealed the difference in structures and rheological properties of hydrogels synthesized under different conditions. The insights obtained from this analytical method can be applied to guide the manufacturing process to generate HA hydrogel of "tailored" structures for different application scenarios.