It has been challenging to design seedling pick-up mechanism based on given key points and trajectories, because it involves dimensional synthesis and rod length optimization. In this paper, the dimensional synthesis of seedling pick-up mechanism with planetary gear train was studied based on the data of given key points and the trajectory of the endpoint of seedling pick-up mechanism. Given the positions and orientations requirements of the five key points, the study first conducted a dimensional synthesis of the linkage size and center of rotation. The next steps were to select a reasonable solution and optimize the data values based on the ideal seedling trajectory. The link motion was driven by the planetary gear train of the two-stage gear. Four pitch curves of noncircular gears were obtained by calculating and distributing the transmission ratio according to the data. For the pitch curve with two convex points, the tooth profile design method of incomplete noncircular gear was applied. The seedling pick-up mechanism was tested by a virtual prototype and a physical prototype designed with the obtained parameter values. The results were consistent with the theoretical design requirements, confirming that the mechanism meets the expected requirements for picking seedlings up. This paper presents a new design method of vegetable pot seedling pick-up mechanism for an automatic vegetable transplanter.