The coupling form of the polymeric-inorganic component and the relation between intermolecular special hydrogen bonding interaction and the microstructure of crystallizable polymer, as well as micro-phase separation scale in non-covalently coupled poly (epsilon-caprolactone) (PCL)/silica (SiO2) hybrid materials were investigated by means of Fourier transform infrared (FTIR) spectroscopy, ultraviolet-visible (UV-Vis) spectroscopy, wide angle X-ray diffraction (WAXD) and differential scanning calorimetry (DSC). The results show that the coupling form between PCL and SiO2 mainly depend on a strong intermolecular hydrogen bonding interaction in the hybrid system. The hydrogen bonding strength increases with increasing TEOS content, while the crystallization of PCL decreases, and the optical transparency of hybrid materials increases. In addition, it affects the scale of micro-phase separation in hybrid materials.