In order to achieve the separation of three different motion driving systems, which are seedling fetching, plant moving and seedling planting on potted-seedling automatic transplanter, simplify the mechanical transmission system structure, and improve the reliability and quality of operations, a potted-seedling automatic transplanter control system for motion coordinating was designed based on PLC. This system accomplishes synchronous coordination of seedling disk lateral feeding motion driving by stepper motor, seedling fetching manipulator longitudinal reciprocating motion driving by servo motor, control of pneumatic perpendicular fetching/casting seedling motion of seedling fetching manipulator and pneumatic feeding seedling motion, and mechanical driving planting motion, which simplifies the mechanical transmission system, at the same time, further raises the positioning precision of the seedling fetching and the seedling moving flexibility, reduces the loss of the seedling matrix and improves the transplanting effect. The working principle of potted-seedling automatic transplanter is expounded, the design of hardware system and software system of the motion coordination control system is discussed in detail, and the actual transplanting test is carried out. Experimental results show that under the control of motion coordination control system, potted-seedling automatic transplanter can achieve 40 strains/(min·row) fetching/casting seedling rate, at the overall single row transplanting average rate of 39.9 strains/min, prototype completes fetching/casting seedling process, ultimately, the success rate of feeding seedlings into planting device is 96.9%.