Rice straw in the fields of the middle and lower reaches of the Yangtze River exhibits high stubble retention and a substantial straw volume. The interaction between straw and tools are complicated and have a significant impact on the performance of straw incorporation implement. The lack of accurate rice straw model by discrete element method (DEM) limits the analysis of the interaction between straw and tools during the design and optimization of key components of straw incorporation implement. A flexible rice straw model was established by the particle replacement method based on the Hertz-Mindlin with Bonding contact model in DEM. Calibration of the discrete element model and multi-condition experimental verification were conducted. The friction coefficients of rice straw were determined through physical experiments, and the maximum load was measured in the straw bending test as the calibration index. The Plackett-Burman experiment and the steepest ascent experiment were used to select significant factors and their optimal value ranges for the flexible model, and the optimal parameter combinations for significant factors of the straw bonding model were determined by Central-Composite tests. The result was the normal contact stiffness was 3.040×1010 N/m3, and the tangential contact stiffness was 2.296×1010 N/m3. The relative error between the maximum load obtained from the simulation with the calibrated parameters and the actual maximum load with the experiment was 1.82%. It indicated the effectiveness of the calibration method. To verify the effectiveness of the above calibration method under different working conditions, the bending test of blades and the rotating cutting test of the rotary blade were conducted. The relative error between the maximum load obtained with the simulation and experiment in the bending test of blades was not more than 4.55%, while the relative error of the maximum torque between the simulation and experiment in the rotating cutting test of the rotary blade was not more than 7.95%. It indicated that the flexible rice straw model by DEM calibrated using the bending test was accurate and effective in simulating straw bending test and rotating cutting of the rotary blade processes and applicable to simulation analysis under the rotary tillage operating conditions. The research provided an effective model and method to analysis of the interaction between straw and tools for the optimization design of key components of straw incorporation implement.