Aiming at the low efficiency and inconsistent quality in manual pre-cutting of solanaceous crop seedlings before grafting, a whole-tray mechanical pre-cutting method was proposed to expand the operational space for subsequent on-tray grafting and improve work efficiency. A novel whole-tray pre-cutting device for solanaceous seedlings was designed, featuring a tilted tray conveyor system and a height-adjustable cutting mechanism. The designed device can adapt to different rootstock and scion varieties. Establishing tissue structure models of tomato, pepper, and eggplant seedlings based on microscopic imaging, as well as models of different blade angles by ANSYS, and simulate the cutting effects of different blade angles on seedlings. The simulation results showed that a cutter with a 30°blade angle produces the smoothest seedling cross-sections. To further validate the device's performance, entire trays of tomato, pepper, and eggplant seedlings were subjected to a four-factor, three-level response surface analysis experiment by using Design-Expert. The experimental results indicated that the best pre-cutting effect was achieved under the parameters of conveyor speed at 0.3m/s, cutting rate at 0.633m/s (motor speed: 3500r/min), air-blowing angle at 140°, and air pressure at 0.5MPa. The average success rate of pre-cutting is 98.9%, and the processing efficiency is 600 trays per hour (for 72cell trays). This study can provide certain technical and experimental bases for the research and development of the pre-cutting device of the grafting machine.