Aiming at the problems that tomatoes are fragile and the traditional end-effector design is not suitable for tomato picking, a combination of the bionic principle of FRE structure and finger design was proposed. Based on the physical properties of tomatoes, a flexible underactuated end-effector for tomato picking and sorting was designed. The optimal structural parameters of fingers were determined by finite element analysis, and the tomato grasping experiment was carried out. The results show that the flexible end can grasp and transport tomatoes with diameters ranging from 65 to 95 mm without damage, which can withstand 7 N tensile force, the load is more than 2 times of its own weight, the tomato coverage rate is greater than 23.6%, and the effective grab rate is 100% and has the advantages of the strong stability, universality, and protection. The research provides a novel solution for the design and application of the tomato picking and sorting robot end-effector.