In the field of harvesting machinery, it is advantageous to consider the characteristics of crops in the design stage rather than through actual mechanical tests especially in terms of reducing costs and shortening the development cycle. By establishing a dynamic model that considered the vibration response characteristics of flexible crop stems, it was of great significance to explore the separation mechanism of grains and grass, analyze the grains separation process and optimize the parameters of the combine harvester. A dynamic simulation method for flexible crop stem was proposed, and the dynamic response characteristics of crop stem were studied. Firstly, the dynamic model and dynamic simulation method of crop flexible stem were given. Taking the third internode of the mature wheat as an example, important parameters such as the inner and outer diameter, unit mass density and elastic modulus of the stem were measured. Then, by simulating the lateral and longitudinal vibration characteristics of the stem, the basic dynamic response characteristics of the stem were studied, and the reliability of the simulation was verified by comparing with the theoretical calculation results. The lateral vibration frequency and longitudinal vibration frequency of the wheat stems with a length of 108mm, an outer diameter of 3.7mm, an inner diameter of 1.9mm, and a Young’s modulus of 5.27GPa obtained by simulation were 164.28Hz and 7633.59Hz, respectively. The relative errors of the theoretical calculation results were 0.28% and 0.12%, respectively. Finally, the practicability of the flexible stem model was verified by simulating the separation experiment. The simulation results were in good agreement with the theoretical calculation results.