Sequential interpenetrating polymer networks (IPNs) were prepared using polyurethane (PUR) synthesized from canola oil-based polyol with terminal primary functional groups and poly(methyl methacrylate) (PMMA). The properties of the material were evaluated by dynamic mechanical analysis (DMA), differential scanning calorimetry (DSC), and modulated differential scanning calorimetry (MDSC), as well as tensile properties measurements. The morphology of the IPNs was investigated using scanning electron microscopy (SEM) and MDSC. A five-phase morphology, that is, sol phase, PUR-rich phase, PUR-rich interphase, PMMA-rich interphase, and PMMA-rich phase, was observed for all the IPNs by applying a new quantitative method based on the measurement of the differential of reversing heat capacity versus temperature from MDSC, although not confirmed by SEM, most likely due to resolution restrictions. NCO/OH molar ratios (cross-linking density) and compositional variations of PUR/PMMA both affected the thermal properties and phase behaviors of the IPNs. Higher degrees of mixing occurred for the IPN with higher NCO/OH molar ratio (2.0/1.0) at PUR concentration of 25 wt %, whereas for the IPN with lower NCO/OH molar ratio (1.6/1.0), higher degrees of mixing occurred at PUR concentration of 35 wt %. The mechanical properties of the IPNs were superior to those of the constituent polymers due to the finely divided rubber and plastic combination structures in these IPNs.