In this paper, we report a new design and fabrication of an integrated two-layer phase mask for five-beam holographic fabrication of three-dimensional photonic crystal templates. The phase mask consists of two layers of orthogonally oriented gratings produced in a polymer. The vertical spatial separation between two layers produces a phase shift among diffractive laser beams, which enables the holographic fabrication of inter-connected three-dimensional photonic structures. A three-dimensional photonic crystal template was fabricated using the two-layer phase mask and was consistent with simulations based on the five beam interference. The reported method simplifies the fabrication of photonic crystals and is amendable for massive production and chip-scale integration of three-dimensional photonic structures.