Liquid crystals (LCs) are an intermediate phase between a solid and a liquid phase, and have features of both solid ordering and liquid fluidity. LC materials have been employed as electronic materials in the LC display industry because they exhibit optical and electromagnetic anisotropy, and thus have a very sensitive response to external fields. In the past, the aim in electro-optical devices was to improve performance by eliminating LC defects. However, after their potential as a new type of self-assembling building block was demonstrated, methods for controlling LC defect structures have been intensively studied. In this Ph.D. dissertation, we mainly discuss the morphogenesis and control of LC defect structures in antagonistic boundary conditions that induce the elastic deformation of LC molecules, to form defects. To this end, in the dissertation we suggest systems that can variously modify the antagonistic boundary conditions. The morphogenesis of defects was studied using thermal phase transitions with a fluid substrate. In addition, surface modification of the substrate and an in-plane electric field were used to variably control defect structures. We showed various arrangements of nanoparticles as an application, based on the controlled defects. Finally, micron-sized air pillars with adjustable shapes and surface properties were introduced to control defect formation and, moreover, the morphogenesis of the defects formed by flowing LC materials was investigated.