The invention discloses a deformation ellipse-circular gear back planting rotating type transplanting mechanism of a walking transplanter. A left and a right gear boxes with the same internal structure are respectively fixed on the shaft ends extending outside a chain wheel box from a center shaft, wherein center deformation ellipse gears fixed on the chain wheel box through a left and a right flanges are respectively arranged on both ends of the center shaft in the gear boxes; the left and the right center deformation ellipse gears drive middle circular gears fixed with the left and the right middle deformation ellipse gears on a left and a right middle shafts to rotate through the left and the right middle deformation ellipse gears fixedly arranged on the left and the right middle shafts; the left and the right circular gears are engaged with a left and a right planet circular gears fixedly arranged on a left and a right planet shafts; and planting arm parts are fixed on one ends ofthe left and the right planet shafts extending from the gear box. Only one set of planet gears in the gear boxes are used for transmission relative to the center deformation ellipse gears to drive one planting arm to move. The mechanism has a buckle-shaped track to have a small planting pit so as to meet the requirement for rice planting.