Aiming to address the problem of severe kernel damage caused by high-frequency, intense impacts from threshing elements during corn grain direct harvesting using conventional rotary drum threshing devices, a low-damage threshing strategy was proposed. The strategy involved first pre-fragmenting intact ears into segments to loosen the kernels, then placing these ear segments between upper and lower threshing boards. Threshing was achieved through reciprocating flexible rubbing, avoiding rigid impact on the kernels. Based on this approach, a low-damage vibrational threshing device for fragmented corn ears was designed where ear fragment were processed between reciprocating boards equipped with flexible polyurethane and reinforced nylon elements to minimize impact stress. Through theoretical analysis, the main structural and operational parameters of the device were determined, and a vibration dynamic model for the interaction between the threshing device and corn fragments was established. Using the exit board spacing, upper board frequency, and lower board frequency as experimental factors, and threshing efficiency and damage rate as evaluation indicators, a three-factor, three-level Box Behnken experimental design was implemented. Variance analysis of the results was performed, and regression models were used for parameter optimization. The optimal parameters were determined as follows: exit board spacing of 13.6 mm, upper board frequency of 12.9 Hz, and lower board frequency of 37.6 Hz. Verification tests under this parameter combination yielded an average threshing efficiency of 97.66% and an average damage rate of 1.96%. These results were largely consistent with the regression model optimization results and met the requirements for low-damage corn threshing.