We have investigated the role of microphase segregation as the driving force in the stabilization of thermotropic ionic liquid crystals of smectic type. To this end we have applied the heterogeneity order parameter, initially proposed for ionic liquids, to the coarse-grained molecular dynamics simulation results for a model system of an imidazolium nitrate ionic liquid crystal, [C(16)mim][NO3], whose phase diagram was recently studied. We have found that the heterogeneity order parameters become larger when the system goes through the transition from the isotropic phase to the smectic A phase as the temperature decreases. This can be understood by considering that, in the smectic A phase, the layered structure allows the tail groups to have a degree of aggregation larger than that in the isotropic phase. Our results highlight the role of microsegregation in the stabilization of ionic liquid crystals, which cannot be revealed by the commonly used translational and orientational order parameters used to describe liquid crystal phases.