The greenhouse plug seedlings transplanting machines applied to industry are mostly with three-dimensional gantry structure. There are some obvious shortcomings like large size and inertia, low relatively rigidity, high prices and poor flexibility in operating capacity and not suitable for filling the gaps with seedlings or rejecting seedlings in high-speed operation. In view of these problems, it was intended to design a transplanting machine system with main body of parallel mechanism. The main structure of parallel transplanter and its five kinds of end effector of matching design were introduced. And then the quality of these end effectors was calculated. First of all, the rigid-flexible coupling multi-body dynamics model of parallel mechanism was established in ADAMS. Secondly, a longest diagonal trajectory was picked for simulation, and the error between the theoretical trajectory of the rigid model and the actual trajectory of the flexible model was compared. And then, the influence of changes of mass to motion error was set and explored by rigid-flexible coupling multi-body dynamics simulation in ADAMS and the feasibility of the parallel design was verified. It was found that there was oscillation at the end of the transplanting track. Finally, the positioning accuracy was tested by the physical prototype. Position error of the moving platform to each point was counted and the control system was compensated. It was turned out that the average positioning error was reduced from 7.611mm to 1.208mm. And most of the errors were systematic errors. During working process, the transplanting machine was with low deformation and high accuracy in taking and delivering stage during acceleration peak was 20m/s2 and average speed was 2m/s. But when the average speed was 3m/s and the acceleration peak was 30m/s2, the error was increased and the radial support force needed to be improved.