The discrete elemental parameters of pod pepper seeds were calibrated for future numerical optimization of the pod pepper seed cleaning device. The study concentrates on calibrating the intrinsic and contact parameters of pod pepper seeds utilizing the discrete element method. Compression tests were performed to ascertain intrinsic parameters such as Poisson’s ratio and the seeds’ elastic modulus. The static friction coefficient and collision restitution coefficient between the seeds and steel plates were identified through incline and free-fall tests. Plackett–Burman, steepest ascent, and Box–Behnken experiments were performed to establish a second-order regression model correlating significant parameters with the angle of repose. The optimal parameter combination, based on the measured angle of repose (32.45°), yielded static friction coefficients between seeds, rolling friction coefficients between seeds, and static friction coefficients between seeds and steel plates of 0.608, 0.018, and 0.787, respectively. The two-sample t-test of the physical and simulated repose angles yielded p > 0.05, and the relative error of the physical and simulated repose angles was 0.68%, which confirmed the reliability of the calibration parameters. The findings indicate that the calibration method for pod pepper seeds effectively informs the calibration of parameters for other irregular crops.