We report a combined holographic and nanoimprinting lithography technique to produce three-dimensional woodpile photonic crystal templates through only one single exposure. The interference lithography process uses an integratable diffractive optical element for large throughout 3D pattern manufacturing. The diffractive optical element consists of two layers of phase grating separated by an intermediate layer, fabricated by repeated nanoimprinting lithography, followed by an SU8 photoresist bonding technique. Grating periods, relative orientation, diffraction angle, and efficiency, as well as layer to layer phase delay, are well designed during manufacturing. By thermally optimizing the thickness of the intermediate layer, this paper demonstrates the fabrication of interconnected 3D photonic structures with arbitrary symmetry through a single laser exposure. The two-layer phase mask approach enables a CMOS-compatible monolithic integration of 3D photonic structures with other integrated optical elements and waveguides.