The liquid crystal spatial light modulator (LC-SLM) is able to provide flexible wave front control, whereas its phase response distortions will influence the modulation accuracy. In this paper, we will provide a novel sub-regional phase response calibration method for minimizing these distortions. In our calibration method, the entire panel is divided into several local regions based on the similarity of phase response characteristic. Liquid crystal cells in one sub-region show the same phase response. The calibration method is theoretical analyzed and experimentally verified. For the entire Jasper 4K SLM panel, when three local regions are built, the root mean error of linear phase shifts is reduced to approximate 0.1 rad. The calibrated SLM is applied for holographic display and the structural similarity index of the assessment shows the improvement ratios reach 30.6%, 62.5%, and 43.6% for R, G, and B reconstructed components respectively. It also could be used for the calibration of various SLMs in the future.