Usually the planters used in agricultural machinery face two problems: The planters have to spread the soil twice using the tray seed planter, and it is difficult for them to dig the holes before planting. This study has designed a spiral digging end-effector to dig holes in parallel effectively and quickly so that the seeds can be planted in the holes easily. A spiral digging end-effector was designed with five spiral bits, a synchronous belt, a cylinder, a gear motor, and a connecting plate based on the tray size and the pumpkin seed characteristics. Before the optimization of the end-effector’s parameters, the substrate discrete element model parameters were calibrated using the method of “material funneling” applied for the EDEM discrete element model simulation. The contact parameters and model parameters (substrate–substrate static friction coefficient, substrate–substrate rolling friction coefficient, and surface energy) that have significant impacts on the substrate AOR (angle of repose) were selected by applying the Plackett–Burman Design and the path of steepest ascent method, and their respective optimal value range were determined. The optimal parameter values were obtained through the Central Composite Design response surface analysis test, and the parameters of the spiral digging end-effector were optimized combining the substrate particle simulation. The verification test results indicate that the substrate discrete element model parameters were accurate and reliable if the substrate static friction coefficient was 0.427; the substrate rolling friction coefficient was 0.039, and the surface energy was 0.228. When the cone angle is 30°, the spiral angle is 80°, and the rotational speed is 240 r/min, the section width at the hole depth of 13 mm is 23.1 mm, and the particle overflow proportion is about 2.05%. Compared with the protrusions penetrating end-effector, soil porosity is increased, and soil aeration is improved. Therefore, the spiral digging end-effector can effectively and quickly dig holes in the seedling substrate and can sow pumpkin seeds, which provides a research basis for the design and improvement of automatic pumpkin seed sowing equipment.