Purpose <p>Position-sensitive detectors play a crucial role in gamma-ray imaging systems. To enhance the detector’s inherent spatial resolution, one promising technique involves the phoswich design, which combines pixelated scintillators with different decay times.</p> Method <p>In a previous study, we constructed a phoswich detector comprising a side-by-side GAGG-F/GAGG-T scintillator array coupled to an 8 × 8 SiPM array. Traditionally, all pulses are distinguished using a parameter with a global cut value. However, due to the non-uniformity of the array, pulse shapes vary with the interaction position of the gamma-ray. In this paper, we propose a novel procedure for crystal discrimination. Initially, the crystal flood map with all events is roughly segmented. Subsequently, the crystal discrimination values of each zone are histogrammed to generate the cut value for each zone. Following this, flood maps of GAGG-F and GAGG-T are generated using these cut values. Finally, flood maps of GAGG-F and GAGG-T are segmented, respectively.</p> Results <p>The novel procedure is compared with the traditional procedure, with results demonstrating that the novel procedure improves pulse discrimination.</p> Conclusion <p>In conclusion, the crystal discrimination for position-sensitive gamma-ray detectors can be enhanced by incorporating interaction position information.</p>