Interference lithography is a promising method for fabricating large-area, defect-free three-dimensional photonic crystal structures which can be used for facilitating the realization of photonic devices with a fast processing time. Although they can be used in waveguides, resonators, and detectors, their repeated regular array patterns can only be used for limited applications. In this study, we demonstrate a method for fabricating large-area photonic crystal structures with controlled defects by combining interference lithography and two-photon lithography using a light-curable resin. By combining regular array structures and controlled patterns, monotonous but large-area regular structures can be obtained. Furthermore, the patterned structures have considerable potential for use in various applications, such as solar cells, sensors, photodetectors, micro-/nano-electronics, and cell growth.