Potted-seedling transplantation has great significance in agriculture production. At present, potted-seedling transplanting in dryland production is accomplished by the seedling pick-up mechanism and the seedling planting mechanism. The seedling pick-up mechanism must achieve the function of picking up seedlings from the plug tray in an orderly manner and delivering seedlings to the seedling planting mechanism; the design of such a mechanism is challenging, and the efficiency and performance of the existing seedling pick-up mechanism are not perfect. The relationship between the olecranon-shaped trajectory of the noncircular planetary gear mechanism and the transmission ratio of the noncircular gear was illuminated in previous research. The seedling pick-up mechanism in the form of double manipulators controlled by a second-order free noncircular planetary gear system was studied in this article. The trajectory and attitude requirements allowing the seedling pick-up claw to attain the required motion were analyzed in detail, the mechanism’s ideal movement objectives were proposed, and the parameters of the transmission ratio and mechanism structure were optimized. A prototype was produced to carry out the experiment, and the optimal combination of rotational speed of the mechanism, seedling pick-up azimuth angle, clamping quantity and seedling pick-up depth were found. The research results show that the seedling pick-up mechanism of a second-order free noncircular planetary gear system is efficient and is a better choice for the seedling pick-up mechanism used in potted-seedling transplantation in dryland production.