The phase structure of poly(ethyl methacrylate)-polyurethane (PEMA/PUR) interpenetrating polymer networks (IPNs) has been investigated by means of modulated-temperature differential scanning calorimetry (M-TDSC), dynamic mechanical thermal analysis (DMTA) and small-angle X-ray scattering (SAXS). Experimental data from both M-TDSC and SAXS indicate that the morphologies of all the PEMA/PUR IPN samples (90 : 10 to 10 : 90 PUR/PEMA) are multi-phase structures. The scattering peaks from SAXS are quite broad, thereby indicating a distribution of microdomain sizes from 5 to 12 nm. This structure formation in IPNs is a competitive process between phase separation and the formation of cross-links which restricts segmental diffusion. An M-TDSC-based characterization method for IPNs has been developed using the differential of heat capacity signal, dC(p)/dT, to analyze phase structure and calculate the weight fraction of each component.