The invention provides a novel seedling grafting device and a grafting method thereof. The novel seedling grafting device comprises a rack, a clamping mechanism and a shearing mechanism, wherein the rack comprises a clamping mechanism mounting plate, the clamping mechanism comprises a clamping jaw air cylinder, a clamp head, a guide column and a seedling combining air cylinder, the clamping jaw air cylinder is installed on the clamping mechanism mounting plate, and drives the clamp head to conduct opening motion and closing motion, the seedling combining air cylinder is installed on the clamping mechanism mounting plate, and forward pushes the clamp head and the clamping jaw air cylinder, and the shearing mechanism comprises an abutting lifting air cylinder, a shearing air cylinder, a blade and a seedling placing groove; the shearing mechanism is arranged in front of the clamping mechanism, the abutting lifting air cylinder drives the shearing mechanism to move up and down, the seedling placing groove corresponds to the opening of the clamp head, the blade is arranged beside the seedling placing groove, and the shearing air cylinder drives the blade to move toward the seedling placing groove. According to the novel seedling grafting device, through the adoption of the clamping mechanism and the shearing mechanism, grafting can be completed within a short time, and the survival rate after grafting can be drastically increased.