Glycosaminoglycan-based biohybrid hydrogels represent a powerful class of cell-instructive materials with proven potential in tissue engineering and regenerative medicine. Their biomedical functionality relies on a nanoscale polymer network that standard microscopy techniques cannot resolve. Here, we introduce an advanced analytical approach that integrates transmission electron microscopy, X-ray scattering, and computer simulations to directly and quantitatively characterize the nanoscale molecular network structure of these hydrogels. This method provides detailed insights into network connectivity and inhomogeneities, which are critical factors for understanding their functional properties and the cell-instructive cues they determine. Given that the glycosaminoglycan-based hydrogels facilitate the controlled delivery of soluble growth factors and guide the growth of complex organoid cultures, our approach also illuminates essential aspects of cell-material interactions and remodeling processes. Ultimately, this integrated strategy enables the precise customization of engineered matrices for regenerative therapies and disease/tissue modeling.