Abstract In this paper, it is described the design of seedling separation device with reciprocating movement of seedling cups and control system of the full automatic plug seedling transplanter. The analysis of the research indicates that the specific strategic path seedling is plane and corresponding control system is formulated. It is put forward special intention on the specific designing of the main components (transplanting device, seedling device and seedling cup) of the seedling separation device. The linear driving motor and driving cylinder are used to control the reciprocating motion, open and close mechanism of mobile seedling cups. The control schemes of the seedling picking, seedling transmission and seedling dropping are designed in detail. It is assured the control program of picking of seedling in the fixed position and the transmission of seedling rapidly and dropping of seedling in the fixed position. The positioning accuracy tests of the linear transmission device and the success rate tests of the seedling device are carried out separately. It is found that the positioning accuracy of a linear transmission device decreased gradually with the increase of seedling speed, especially when the motor pulse frequency exceeds 20,000 Hz. The motor gets out of steps and the precision will drop rapidly. After that it is optimized the motor by setting different pulse frequencies, and fix the range of error values between 0.2 mm and 0.8 mm which is according to the requirement of seedling location. The results of seedling tests of seedling device indicate that the qualified rate of seedling decreases gradually with the increase of seedling speed and the success rate of 70 working cycles/min is 95.03%. This demonstrates that the structure of mechanical components of seedling separation device meets the sub-seed movement requirements. The optimization of the control system could increase the position accuracy according to requirements and achieve the goal of automated sub seedlings.