In order to enhance the accuracy of discrete element numerical simulations in the processing of small-seed particles, it is essential to calibrate the parameters of seeds within the discrete element software. This study employs a series of physical tests to obtain the physical and contact parameters of red clover seeds. A discrete element model of red clover seeds is established. Plackett–Burman Design, steepest ascent, and Central Composite Design experiments are sequentially conducted. The simulation deviation of the resting angle of red clover seeds is employed as the evaluation criterion for parameter optimization. The results indicate that the coefficients of static friction between red clover seeds, the coefficients of rolling friction between red clover seeds, and the coefficients of static friction between red clover seeds and the steel plates significantly influence the resting angle. Modeling was performed using a backpropagation neural network, a genetic algorithm–optimized BP network, particle swarm optimization, and simulated annealing. It was found that GA-BP ensured both accuracy and stability. Compared to the traditional response surface methodology, GA-BP showed better fitting performance. For the optimized red clover seed simulation, the error between the angle of repose and the physical experiment was 0.98%. This research provides new insights into the calibration of small-grain seed parameters, demonstrating the value of GA-BP for precision modeling.