A detailed heterogeneous model considering the thermodynamic incompatibility was developed to simulate polyurethane/poly(methyl methacrylate) (PU/PMMA) interpenetrating polymer network (IPN) formation. The Gibbs free energy was calculated to predict the phase separation point and a two‐film theory was used to quantify the mass transfer between the PU‐rich phase and the PMMA‐rich phase. Compared with the homogeneous model, the cross‐linking density of PMMA increases rapidly during the network formation, because the monomer dispersion in two phases improves the possibility of free radical cross‐linking reaction, whereas the cross‐linking density of PU is unaffected. Simulations show that the partitioning of monomer significantly affects the PMMA network structure. The phase separation is strongly dependent on the onset of MMA polymerization. The proposed model allows visualizing of the IPN formation process and provides direction for reducing the extent of phase separation. Moreover, the structural information derived from the simulations can be further related to the properties.