Aiming at the problem of high loss rate and high impurity rate of tubers due to incomplete fruit impurity separation during the mechanised harvesting of tiger nuts, a double-deck roller sieve type fruit impurity separation device was designed. The main structure and working parameters of the fruit impurity separation device were determined through theoretical analysis. A coupled EDEM-MBD simulation model of separation device-harvest material interactions was established. A three-factor, three-level simulation experiment was carried out based on the Box-Behnken test principle, using the rotation speed of the double-deck roller sieve, the rotation speed of the separation auger, and the length of the flexible tooth area as test factors, and tuber separation rate and impurity rate as test indicators. An ANOVA was conducted on the test results and a regression model was established between the separation rate, impurity rate and each significant factor, and the regression model was used to search for the best parameters. The results showed that the three factors all had significant effects (P<0.01) on the separation rate and the impurity rate;when the rotating speed of the double-deck roller sieve was 24.9r/min, the rotating speed of the separation auger was 148.5r/min and the length of the flexible tooth area was 1277.8mm, the maximum separation rate was 96.23% and the minimum impurity rate was 25.55%. The results of the field validation tests showed that the average separation rate of the fruit impurity separation device under the best combination of parameters was 93.19% and the average impurity rate was 26.65%, which were basically consistent with the optimal results of the regression model;when the fruit impurity separation device was used in combination with the cleaning device, the separation rate was increased by 1.05 percentage points and the impurity rate was reduced by 9.97 percentage points, which could meet the working requirements of the tiger nut harvester.