During the greenhouse seedling tray cultivation process, phenomena such as missing seedlings and poor seedling development occur, necessitating the elimination and replanting of substrate in cavities with missing seeds or stunted growth to enhance yield. To address the challenge of eliminating low-quality seedlings in greenhouse seedling trays, a negative pressure elimination device was designed based on the physical parameters of the seedling tray substrate. Considering the tendency of low-quality seedling substrate to cause pipeline blockages during negative pressure elimination, a swirling flow anti-clogging method was implemented by incorporating a threaded structure at the end tube. Pre-experiments identified key factors affecting elimination success rate and pipeline blockage rate in the end tube structure: the cross-sectional shape of internal threads and the parameter range of thread turns. A Fluent EDEM coupled simulation method was employed to investigate the impact of these factors on substrate fragmentation. Response surface analysis was used for experimental validation, with a three-factor, three-level test design focusing on thread cross-sectional shape, number of thread turns, and end tube lifting speed. Optimization targeting elimination success rate and blockage rate revealed the optimal parameter combination: triangular internal thread cross-section, eight thread turns, and a lifting speed of 0.13 m/s. Finally, using the optimized parameters mentioned above, a defective seedling adsorption test was conducted. The results showed a seedling removal success rate of 99.4% , a blockage rate of 0.01% , meeting the requirements of the seedling tray for subsequent replanting operations.