During the process of automatic picking, malfunctions caused by collisions between the picking manipulator and obstacles can damage plants and/or injure staff. To solve this problem, a flexible joint based on an elastic actuator is designed. Using a collision detection algorithm based on monitoring the current, a feedback control system with a flexible joint moment is set up, and a protection mechanism for the staff and plants against collisions with the manipulator during the automatic picking process is established. The results of the experiments on a prototype show that the proposed feedback control system with flexible joint moment can detect collisions of the manipulator with high accuracy. Based on the jump value of the current during collision detection, the impact moment on the flexible joint is estimated to have a minimum resolution of 2.444 × 10 −3 N•m. The frequency of collision detection is 37 Hz, and the minimum estimation error in the impact moment of the flexible joint is 2.25%.