Combined with the harvesting mode and frequently-used rod-type separation devices in the main potato production areas of northern China, a disturbance separation device for potato harvester was designed to solve the problems of the poor soil fragmentation efficiency and harvest quality which existed in small-scale potato harvesters. On the basis of explaining the overall structure and working principle, combined with the analysis of the collision characteristics of potatoes and the fragmentating process of soil, the main factors which affected the the damage of potatoes and soil fragmentating were obtained. A simulation model was built through EDEM-RecurDyn coupling. The optimal number of disturbance rods obtained from single factor experiments was 4. The experimental factors were disturbance depth, eccentric wheel rotary speed, and eccentricity, and the collision force of potatoes and soil fragmentation rate were used as evaluation indicators. The method of Box-Behnken central combination design was used to conduct simulation experiments and work at the variance analysis on the experimental results. The response surface methodology was used to analyze the influence of various interaction factors on the experimental indicators. The optimum value of the influencing factors was determined based on actual operating conditions. The experiment showed that when the operating speed of the separating sieve of the harvester was 0.7m/s, the disturbance depth was 51.5mm, the rotary speed of the eccentric wheel was 2.3r/s set by the governor and the eccentricity was 31mm, the fragmentation rate of soil was 60.7%, and the average of the peak impact acceleration values collected by the impact recording device was 790.66m/s2. Both were below the critical damage threshold of potatoes.