Water-surfactant-oil ternary systems have various phase behaviors and substructures that depend on their chemical composition and component ratio. These substructures can be used as templates for the synthesis of a variety of nanostructures. In this study, the phase behavior of a pseudoternary system consisting of aqueous urea-cetyltrimethylammonium bromide (and n-butanol)-cyclohexane is analyzed. Additionally, wrinkled silica mesostructures (WSMs) with various morphologies are synthesized using the microemulsion layer in the multiphase areas of the pseudoternary system with restricted degrees of freedom as a template. The particle size of the wrinkled silica nanoparticles (WSNs) and the connective morphology of the WSMs can be controlled via the catalytic conditions. In addition, some materials that are difficult to produce, such as radially branched WSNs and shuttlecock-shaped Janus nanoparticles, are prepared using a gradual seed-growth mechanism of silica in the emulsion system.