We report the effect of physical properties, such as flexibility and polymer density, of nanogel particles (NPs) on the association/dissociation rates constant (kon and koff) and equilibrium constants (Kd) of multipoint protein recognition process. NPs having different flexibilities and densities at 25 °C were synthesized by tuning cross-linking degrees and the volume phase transition (VPT) temperature. Rate constants were quantified by analyzing time course of protein binding process on NPs monitored by a quartz crystal microbalance (QCM). Both kon and koff of swollen phase NPs increased with decreasing cross-linking degree, whereas cross-linking degree did not affect kon and koff of the collapsed phase NPs, indicating that polymer density of NPs governs kon and koff. The results also suggest that the mechanical flexibility of NPs, defined as the Young's modulus, does not always have crucial roles in the multipoint molecular recognition process. On the other hand, Kd was independent of the cross-linking degree and depended only on the phase of NPs, indicating that molecular-scale flexibility, such as side-chain and segmental-mode mobility, as well as the conformation change, of polymer chains assist the formation of stable binding sites in NPs. Our results reveal the rationale for designing NPs having desired affinity and binding kinetics to target molecules.