Abstract: Technology of seedling transplanting is widely used in the tomato planting in Xinjiang, Western China. In recent years, the demanding for the automatically transplanting machine increases rapidly, with the continuous expansion of planting scale. Nevertheless, most transplanting machines used in Xinjiang are semi-automatic transplanters, which still need the manual operation to complete seedling picking and dropping. Thus, it is very imperative to develop the automatic transplanter for the plug seedlings of tomato. As one of the key components in an automatic transplanter, the seedling picking device can pick plug seedlings and then drop them automatically with a preset movement trajectory. Since the stems of tomato plug seedlings have good mechanical properties in a suitable period, in this study, a novel seedling picking device in a stem clipping type was designed for the tomato plug seedlings, using the special mechanism of second-order elliptical planetary gear train and cam swinging rod. An automatic seedling picking test-bed was built for the tomato seedling picking experiment, which was carried out in the Key Laboratory of Northwest Agricultural Equipment of Ministry of Agriculture and Rural Affairs, China. The picking mechanism in a stem clipping type showed a good effect on reducing the damage rate of plug seedling, while improving the efficiency of seedling picking. 1) The kinematic model of seedling picking mechanism was established by analyzing the transmission characteristics of second-order elliptic gear, meanwhile, the actual contour curve of cam was also explored. A specific optimization objective of mechanism parameters was proposed, according to the requirements of picking tomato seedling, and the structural characteristics of seedling picking mechanism. A human-computer interaction optimization software was established on the MATLAB software to optimize the structure parameters for the stem clipping type in a seedling picking device. 2) A dataset on the optimal combination of mechanism parameters was obtained by the human-computer interaction analysis, indicating to satisfy the requirements of oblique clamping and straight pulling operation, when the seedling picking mechanism working. The virtual prototype of seedling picking mechanism in a stem clipping type was designed on the SOLIDWPORKS software, and then the physical prototype of mechanism was developed, according to the optimized structural parameters. 3) The virtual simulation of device and high-speed photography experiment were carried out, in order to verify the accuracy of the optimized structural parameters. The results showed that the relative trajectories at the endpoint of seedling clip captured from a high-speed camera were basically consistent with the theoretical trajectories and virtual prototype simulation. According to the picking experiment of tomato plug seedling, the success rate of seedling picking reached 92%, when the seedling frequency was set as 80 plants/min, while, the damage rate of seedling was only 2.9%, and the success rate of dropping seedlings attained to 94.2%. The test results showed that the seedling picking mechanism was stable and reliable when working, indicating that the mechanism can perfectly meet the agronomic requirements of mechanical seedlings picking for tomato plug seedlings. The findings can provide an important reference and technical support for the development of automatically picking mechanism in plug seedling.