Castor oil (CO) is an environmentally friendly renewable green resource and ideal alternative to petroleum resources. The preparation of high strength and high toughness castor oil-based polyurethane prepolymer (COPU) composites has significant applications such as supporting material and engineering plastic sheet. In this study, unmodified clam shell powder (CSP) with a unique CaCO3-proteoglycan structure was used as a filler to prepare compatible reinforced COPU composite materials. Investigation of the mechanical properties revealed that the elastic modulus of the composite COPU reinforced with 50 wt% of CSP had increased to 5859.0 ± 8.4 MPa representing 187.77% to obtain stiffer and stronger material over pure COPU (2036.6 ± 196.9 MPa). Moreover, the scanning electron microscopy, thermogravimetric analysis and contact angle results demonstrated that the reinforced COPU composites have better compatibility, thermal stability, and water resistance than pure COPU. This work will promote the application prospects of CO-based polyurethane.