In view of the existing problems of the three-arm rice transplanting mechanism, such as the insufficient angle of pushing seedlings, and the partial absolute movement trajectory forward after planting, a reverse design method based on the local motion trajectory was proposed to overcome this problem. Firstly, the relationship between the absolute motion trajectory and relative motion trajectory of the mechanism was analyzed, and combined the existing problems of the original mechanism to preset the return section trajectory of the local standard absolute motion trajectory, the picking-seeding angle to reverse the local relative motion trajectory and key position points of the transplanting mechanism. The non-uniform B-spline curve was used to fit the trajectory. Secondly, a reverse design model for transplanting mechanism was established. A Matlab-based reverse analysis design software for seedling transplanting mechanism was developed to solve the parameters that met the design requirements of the mechanism. At last, the structure of three-arms rotary rice seedling transplanting mechanism was designed, and a physical prototype of the mechanism was manufactured. A virtual kinematic simulation and high-speed photographic kinematics bench test of the seedling transplanting mechanism were carried out to study the motion characteristics of the physical prototype of the mechanism. The results showed that the simulation trajectory, test trajectory and theoretical trajectory were basically the same, and the pushing-seedling angle was increased by more than 9.08°, the return height of the moving trajectory greater than 120mm, the difference between the taking-seedlings and pushing-seedlings’ angle difference and the seedling box’s installation angle was within ±2°, which met the design requirements. The correctness of the design method and design results of the mechanism were verified.