Hydrogels have been developed and applied to various biomedical applications due to their biocompatibility. However, understanding of modulation between cells to hydrogel interface is still unclear, and parameters to explain the interaction are not sophisticated enough. In this report, we studied the effect of polymer chain flexibility on cell adhesion to various hydrogel constructs of collagen and fibrin gels. Specifically, novel method of semi-flexible model-based analysis confirmed that chain flexibility mediated microstructure of the hydrogels is a critical factor for cell adhesion on their surfaces. The proposed analysis showed possibility of more accurate prediction of biocompatibility of hydrogels, and it should be considered as one of the important criteria for polymer design and selections for enhancing both biocompatibility and biofunctionality.