This research explores the correlation between the structural properties of supramolecular biocomposites and their mechanical strength. Hybrid biocomposites composed of surface-modified hydroxyapatite nano-particles and supramolecular polycaprolactone (SP PCL), were prepared at different compositions, and their mechanical, thermal and viscoelastic properties as well as biodegradability, biocompatibility and cytotoxicity were evaluated in vitro. The results were compared with those for SP PCL/naked hydroxyapatite nano-composites. We show that surface modification of hydroxyapatite nanoparticles resulted in outstanding improvement of tensile strength and modulus up to 3.6 and 2.2-fold, respectively. At above 10 wt% HAp and 20 wt% HApUPy, heterogeneous nano-composites with inferior mechanical properties were obtained. Based on rheological (in steady shear mode) and small/wide angle X-ray scattering measurements, unusual improved mechanical properties were ascribed to the formation of supramolecular clusters around nanoparticles. In-vitro degradation of the supramolecular nano-composites was also studied to investigate the overall product biodegradation as well as toxicity of the degradation product(s).