A ductile polycaprolactone (PCL)/modified polyurethane (PU) composite with double mosaic structure was prepared through a novel technology. The composite would be used to reduce waste of resources and the environmental hazards of hogwash oil and expand the application of hogwash oil. Composites with different microstructures were obtained by regulating the proportions of "hard segment-phase" PU and "soft segment-phase" PCL. Meanwhile, the influences of microstructure on the macroscopic physicochemical properties of composites were investigated. Results demonstrated that when the PCL content was 30%, a wrapping structure was similar to "Punica granatum L." and embedded network structure between organic silica-modified PU and PCL were observed in the composite. Owing to the double mosaic structure, the water permeability of the composite was reduced by 61.9% lower than that of modified PU. However, the hydrophobicity of the former was 15.6% higher than that of the latter. The component fixation rate reached 80.8%, resistance to humidity and heat was strengthened. Coated fertilizers were prepared using the composite as the coating material were slightly superior to organic-silica-modified PU in terms of slow N releasing performance. The prepared composite exhibited good physicochemical properties and showed promising application values in many fields, such as coating materials, thermoplastic elastomer and fertilizers. This study provides a novel strategy for preparing porous materials.