To address the challenges of separating roots from soil and the high soil carryover during Ophiopogon japonicus harvesting in heavy clay soils, a variable-gap tooth roller chain rod-and-slat separation device was designed, integrating variable-gap tooth roller soil crushing with vibrating chain rod-and-slat conveying and separation functions. A coupled "soil–plant–equipment" model was established using the discrete element method. Conveying speed, vibration frequency, and amplitude were selected as key operational parameters. Interaction effects were analyzed, and dual-objective optimization was performed using response surface methodology. The contact number was used to characterize soil–plant particle adhesion, while D80 (the distance corresponding to 80% soil fallout) represented spatial distribution characteristics of soil fallout. Optimization results indicate that, within the experimental parameter range, a combination yielding low contact number and low D80 can be achieved. The simulations predicted a D80 of 563.25 mm and a contact number of approximately 6. Conversion of particle-mass data indicated the average soil mass adhering to plants is about 0.0096 kg. Field validation tests conducted at a conveying speed of 0.80 m/s, vibration frequency of 12.00 Hz, and amplitude of 15.00 mm yielded an average soil mass carried by separated plants of 0.012 kg. These results demonstrated that the constructed discrete element model and response surface optimization can be applied to parameter matching for Ophiopogon japonicus root–soil separation equipment, providing a reference for optimizing root–soil separation machinery in hilly and mountainous regions for Chinese medicinal herbs.