Exploiting facile strategy to prepare polyurethane nanocomposites with uniform nanofiller dispersion and desired microphase-separated structure simultaneously is vital for developing high-performance elastomer. Herein, we reported a bio-inspired co-deposition approach for constructing organic-inorganic nanohybrid elastomer to improve interfacial interactions of nanofillers for an optimized microphase-separated structure. In this way, cellulose nanocrystals (CNC) were selected as the nanophase reinforcer, during which gamma-aminopropyltriethoxysilane (APTES)-terminated polyurethane achieved the biomimetic silicification process on CNC surface by assistance with the poly-dopamine (PDA) mediation thus forming a nanohybrid structure in the elastomer. It was found, after the co-deposition process, the dispersion of CNC was markedly improved, and the constructed nanohybrid structure induced multiple physical and chemical interactions within the interior elastomer toward an improved microphase-separated structure as characterized by FTIR, XPS, TG, and AFM measurements. The tensile strength and toughness values of the proposed bio-inspired co-deposited nanohybrid elastomer reached 9.01 MPa and 32.36 MJ/m(3), respectively, marking an increase of 72.3% and 361.6% compared to the CNC-reinforced elastomer. Meanwhile, the construction of organic-inorganic structure also facilitated the thermal stability and water resistance improvement of the resulted elastomers. The design path and model presented here may provide the workable guidance for the synthesis of superior elastomers in further applications.