The practical use of photonic crystals with structural colors requires technology capable of rapidly producing large-area, three-dimensional (3D) periodic nanostructures. Until now, the fabrication of 3D photonic crystals has relied mainly on additive manufacturing and colloidal self-assembly. These technologies have provided a useful academic platform based on precisely controlled 3D periodicity but have not evolved into mass production technology. Here, optical lithography for the rapid fabrication of large-area 3D photonic crystals with structural colors is introduced. The key strategy is to incorporate two orthogonal line gratings (periodicity: 300 nm) made of an elastomer to create a conformal multilevel phase mask. When the mask is irradiated with a 355 nm laser, the five beam interference is established in the proximity region. The interlayer thickness between the two orthogonal line gratings controls the phase difference, which is closely related to the symmetry of the resulting 3D interference pattern. The interlayer thickness is designed to produce a woodpile structure with a planar periodicity of 300 nm and a vertical periodicity of 716 nm. The pattern area of the woodpile photonic crystal is expanded to 1 in(2). Red, green, and blue colors are experimentally realized by controlling the vertical shrinkage of the photoresist.