Ophiopogon japonicus is a major variety of traditional Chinese medicinal herbs, which mainly cultivated in Sichuan Province and Zhejiang Province, and the medicinal part of it is the tuberous root normally barrier underground. Focusing on the labor intensive process of manually removing the tuberous root from Ophiopogon japonicus, as well as the lack of mature mechanical tuberous root removal devices, a tuberous root removal device was specifically designed for Ophiopogon japonicus from Sichuan Province. The device utilized two sets of step type reciprocating cutters, a set of conveying clamping belt, a caliper, and a rack structure. By considering the requirements of the tuberous root of the Ophiopogon japonicus harvesting and measuring the plants' physical parameters, parameters such as overall structure dimensions, caliper interstices, conveying speed, cutting intervals and reciprocating stroke can be determined. The rigid-fliexible coupling simulation analysis between the Ophiopogon japonicus and the tuberous root removal tool was conducted by using ADAMS software. The cutting effect was simulated under the condition of the contact force between the cutting edge and the Ophiopogon japonicus plants exceeded the peak cutting force. The Felx module in ADAMS/view was used to apply flexible treatment to the Ophiopogon japonicas plants, and the changing rules in contact force and plant deformation during the contact collision process was analyzed. Choosing cutting speed, cutting inclination angle and cutting tool configuration as three factors to design a three level orthogonal test. The order of importance for factors affecting cutting effects was as follows: cutting inclination angle, cutting speed, and cutting tool configuration. Cutting speed was significantly correlated with the type of cutting tools. When proceeding high-speed cutting, the peak cutting force generated by the straight-tooth blade tool was greater than that of the other two configurations. Considering the principle of cutting stability reliability, cutting force and tool configuration minimization comprehensively, the optimized solution was carried out: the optimal working parameters was determined as cutting speed of 0.41m/s, cutting inclination angle of 0.3° and a cutting tool configuration of a triangular smooth-edge blade. Verified by simulation, this device had rational structure parameter and met the technical requirements for the harvest of Ophiopogon japonicas tuber, providing a theoretical and experimental references for the further optimization design of mechanical devices.