Aiming at the problem of lack of accurate bonding parameters in the discrete element simulation model of rape shoots stems, which is closely related to the key links of mechanized harvesting of rape shoots stems, such as cutting, transport by clamping, and baling, the stems of mechanized clamping section of rape shoots in the double low rape harvesting period of “oil and vegetable dual-use” were used as research objects. Using EDEM simulation software, a method to construct a discrete element simulation model of double-layer bonding of the middle clamping section stems of the rape shoots was proposed by using three-axis spatial coordinates method. Design-Expert software was used to design the Plackett-Burman test, the steepest climb test and the Box-Behnken test to complete the calibration of the simulation bonding parameters of the clamping section stems of rape shoots. The shear and radial compression models were constructed by using the optimized solutions of calibrated parameters, and the corresponding simulation tests were carried out. The model parameters were further optimized by comparative analysis with the physical test. The results showed that the normal/tangential contact stiffness of inner core to inner core, the normal/tangential contact stiffness of epidermis to inner core, and the normal contact stiffness of epidermis to epidermis had significant effects on the mechanical properties of stems, and the results were 1.94×107N/m, 9.56×108N/m and 6.28×109N/m, respectively. The relative error between simulated values and measured values of all mechanical models was not greater than 3%. And the force change trend of the stem was basically the same, indicating that the optimized calibration parameters were feasible and accurate, and the constructed double-layer bonding discrete method model of stems of rape shoots characterized the difference in mechanical characteristics of its internal structure, which can provide a model basis for the numerical simulation of the related system of stem of rape shoots.