Super-structures produced in the smectic molecular organization are reviewed, and the origin for the structures discussed, in which it is emphasized that the frustration plays an important role in the emergence of the super-structures. Properties and structures of mysterious smectic phases possessing chirality-induced super-structures are introduced, including smectic blue and smectic Q (SmQ) phases that possess three dimensional (31)) structures. The molecular design on stabilizing the 3D structure is proposed. The molecular orientations in the 3D structures are not so sensitive to the external electric field due to an intricate smectic ordering, thus it has been difficult to imagine practical applications of these structures. The SmQ compound possessing an azobenzene core in the molecular structure is designed and the liquid-crystalline properties and photoresponse investigated. By means of the photoisomerization of the azobenzene moiety, we demonstrate that the 3D structure of the SmQ phase can be controlled by light as an external stimulus, suggesting a possibility for new applications utilizing the liquid-crystalline 3D structure.