Recently developed graded photonic super-crystals show an enhanced light absorption and light extraction efficiency if they are integrated with a solar cell and an organic light emitting device, respectively. In this paper, we present the holographic fabrication of a graded photonic super-crystal with a rectangular unit super-cell. The spatial light modulator-based pixel-by-pixel phase engineering of the incident laser beam provides a high resolution phase pattern for interference lithography. This also provides a flexible design for the graded photonic super-crystals with a different ratio of length over the width of the rectangular unit super-cell. The light extraction efficiency is simulated for the organic light emitting device, where the cathode is patterned with the graded photonic super-crystal. The high extraction efficiency is maintained for different exposure thresholds during the interference lithography. The desired polarization effects are observed for certain exposure thresholds. The extraction efficiency reaches as high as 75% in the glass substrate.