This invention belongs to a seedling separating device based on a rack and pinion drive in the field of transplanting machine in the agricultural automation facility, including a rack, a power unit, a linear drive, a number of seedling cups and a cylinder pushing device. The linear actuator is driven by the power unit to move on the frame; these seedling cups are mounted on the linear drive; the cylinder pushing device is mounted on the frame and is located behind the seedling cups and it drives the lower part of the seedling cup to open and retracts to close. The seedling device has simple structure, controllable program and high reliability. The motor drives the seedlings cups to move left and right; the cylinder pushes the cups to be opened and closed; the trust cup is straight down, the seedling attitude is better and the location of seedling can also be adjusted. The device can not only achieve the exact location in the designated seedling, but also to achieve the seedling movement of separating seedlings to two points from the mouth of the seedling cups.