With the aim to solve the problem of seedlings damaged and inefficiency of plug seedlings transplanter, the end-effector was redesigned. According to the actual operational requirements, SolidWorks was used to design the virtual prototype of end-effector. COSMOSMotion was used to analysis trajectory of mechanical finger and COSMOSWorks was used to analysis finite element model of matrix. It showed in motion simulation experiment that the horizontal displacement of the mechanical fingers was mainly affected by the slider displacement (Δh)，while the vertical displacement was mainly affected by the initial angle (α) the mechanical fingers insert in. The forces generated by mechanical fingers distribute in the matrix block edge and won’t damage the seedling stems. The experimental results showed that the success rate of transplanter was 95.76%, the rate of seedlings damaging was 3.06%, and it could meet the operational requirements of transplanting.