In the process of seedling raising in the greenhouse cavity tray, there are phenomena such as seedling leakage and poor growth. In order to ensure the grade of factory seedlings, it is necessary to remove these inferior seedling substrate blocks and replant them with healthy seedlings. The existing end effector for seedling extraction is mainly suitable for large-seedling-aged bowl-body seedlings, and has poor adaptability to small-seedling-aged and weak-rooting bowl-body seedlings. Therefore, a flexible end effector was designed, which suitable for small space seedling planting and its row of multi-end seedling replenishment operation mechanism. The flexible end-effector can be controlled separately, and the claw blades were gradually retracted during the seedling picking process during the descending process, forming a progressive clamping operation on the substrate block. A bunch of red, caryophyllus, begonia, and petunia burrow seedlings were taken as the research objects. Carry out the rigid-flexible coupling dynamic analysis of the flexible end effector for manipulators. The orthogonal experiment of three-factor and three-level seedling transplantation of flexible planting end effector was carried out. The results showed that the experimental factors affecting the seedling root ball intergrity were claw spacing, claw width and substrate moisture content, and the optimal parameter combination was 21mm for claw spacing, 18mm for claw width and 55%~60% for substrate moisture content. Under the optimal combination of parameters, the end-effector seedling transplantation performance verification test was carried out. The results showed that the integrity of the bowl body was more than 85% after successful transplantation, which met the needs of seedling transplantation, and the average seedling replenishment efficiency of the whole machine was 2105 plants/hour (about 68 trays/hour). The research result can provide a reference for the automatic seedling replenishment operation of greenhouse cavity tray seedlings.