High-density transplanting with small plant spacing, small hole size, and large planting depth has strict requirements for hybrid kinematic targets such as the swing angle of the key operation section of the duckbill, the position deviation between the movement point of the mechanism end and the target point, and the trajectory height. Aiming at the poor performance of existing seedling planting mechanisms, this paper carries out the research on the optimization design of single-row two-stage transmission planetary gear train mechanisms with hybrid kinematic design requirements. Taking parameters such as the rotation angle of the first planet carrier, the rotation angle of the middle wheel, the length of the first planet carrier and the end-effector components as optimization variables, and taking the minimum position deviation between the movement point of the mechanism end and the target point and the maximum convexity value of the non-circular gear as optimization targets, the posture angle of the key point, the swing angle of the operation section and the position requirement under the absolute coordinate system are transformed into additional optimization objective functions according to the operation requirements. The multi-objective genetic algorithm is used to solve the problem, and the parameter group of the multi-objective optimization design mathematical model of the mechanism under hybrid kinematic conditions is obtained. According to the seedling planting requirements with the maximum planting depth of 80 mm and the plant spacing of 90 mm, the first planetary carrier and the planting trajectory are obtained through optimization calculation. A prototype was developed and tested on a bench and in a soil bin. The bench test results showed that the average seedling planting success rate was 93.67% and the missed planting rate was 2.33%. The soil bin test results showed that the average seedling planting success rate was 91.42% and the missed planting rate was 3.45%, which met the requirements of high-density transplanting operation.