A rapid design system of cleaning device on rice-wheat combine harvester can improve the design efficiency and quality. As the core part of the system, the reasoning mechanism plays an important role in the system. A reasoning method based on Petri net model was proposed in the rapid design system of cleaning device for rice-wheat combine. Based on the rules and models, a reasoning mechanism to design cleaning devices was constructed to express the parameter transfer relationship by means of the CPN Tools which presents description of Petri net model. Combined the Petri net model with the design knowledge of cleaning device, the design parameters are calculated and transferred by CPN Tools in which the reasoning simulation machine run. According to the reasoning results, the parameterized model library of cleaning device is called to obtain the 3D models of cleaning device parts. The existing experimental verified intelligent design virtual simulation and experimental system are used to simulate the working process of cleaning device. The simulation result shows that the loss rate of the cleaning device is about 1.8 %, and the simulation impurity rate is about 0.9 %, which meets the technical requirements stipulated by the state.