In this paper, we study tunable holographic lithography using an electrically addressable spatial light modulator as a programmable phase mask. We control the phases of interfering beams diffracted from the phase pattern displayed in the spatial light modulator. We present a calculation method for the assignment of phases in the laser beams and validate the phases of the interfering beams in phase-sensitive, dual-lattice, and two-dimensional patterns formed by a rotationally non-symmetrical configuration. A good agreement has been observed between fabricated holographic structures and simulated interference patterns. The presented method can potentially help design a gradient phase mask for the fabrication of graded photonic crystals or metamaterials.