To solve the problem of the high loss rate of threshing devices during the mechanical harvesting of ratoon rice, we propose a method using the principle of rigid–flexible coupling in this paper to reduce losses. Through analysis of the forces and collisions on ratoon rice grains during the threshing process, it has been confirmed that changing the structure and materials of the threshing contact components can effectively reduce grain loss. A rigid–flexible coupling rod tooth was designed, and the overall structural parameters of the device were determined based on force analysis results and dimensional boundary conditions. The MBD-DEM coupling method was used to simulate the threshing process, and the force conditions of the threshing rod teeth and threshing drum were obtained. The influence of the feeding amount and of the flexible body thickness on the crushing of ratoon rice grains was analyzed. In order to obtain the device’s optimal parameter combination, a three-factor quadratic regression orthogonal rotation combination experiment was conducted with drum speed, flexible body thickness, and rod tooth length as experimental factors. The optimization results showed that when the drum speed, flexible body thickness, and rod tooth length were 684 r/min, 3.86 mm, and 72.7 mm, respectively, the crushing rate, entrainment loss rate, and uncleaned rate were 1.260%, 2.132%, and 1.241%, respectively. The bench test showed that it is feasible to use the MBD–DEM coupling method to measure the motion and force of ratoon rice. The rigid–flexible coupling threshing device can reduce the grain crushing rate while ensuring grain cleanliness. Compared with traditional threshing devices, the crushing rate and entrainment loss rate of the rigid–flexible coupling threshing device were reduced by 55.7% and 27.5%, respectively. The research results can provide a reference for the design of threshing devices for ratoon rice harvesters.