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In order to accurately establish a discrete element model for the whole plant flexibility of upright rice during the harvesting period, several physical characteristics, such as geometric features, moisture content, and density, of the entire rice plant were measured, along with frictional properties, such as the static and rolling friction coefficients, and mechanical properties, including the elastic modulus and restitution coefficient. A flexible and upright discrete element model of the rice plant was established using the DEM method based on the Hertz–Mindlin (no slip) and Hertz–Mindlin with bonding mechanical models. The parameters were optimized through Plackett–Burman screening experiments, steepest ascent experiments, and Box–Behnken optimization experiments to accurately determine the discrete element model parameters of each component of the rice plant. The calibration process of the contact parameters between rice grains and steel was analyzed in detail as an example, resulting in a calibration error of 0.68% for the natural repose angle. Taking the calibration of the contact parameters between the main stem and steel as an example, a detailed analysis of the calibration process was conducted. The calibration resulted in a calibration error of 2.76% for the natural repose angle and 2.33% for deflection. This study lays the foundation for understanding the mechanical response of rice and machinery when they are coupled together. Additionally, it provides valuable references for establishing discrete element models of plant species other than rice.