In order to solve the problem of low picking efficiency of single end-effector apple harvesting robot, a structure scheme of multiple end-effectors manipulator was proposed. The mechanical arm, end-effector and manipulator control system were designed. Master-slave two-grade structure was used in the mechanical arm, the multiple end-effectors were linked to forepart of the robot slave mechanical arm, and could operate continuously and simultaneously. The end-effector of the robot had advantages of compact structure and simple drive, which could absorb position error of mechanical arm, and it was universal and suitable for apple, citrus, pears and other spherical fruits picking. According to the characteristics of manipulator with multiple end-effectors, a partitioned fruit tree picking operation strategy was formulated, all the end-effectors picked the target fruits of a picking partition continuously and simultaneously, and the fruits were centrally collected. On this basis, the kinematics mode for robot manipulator was established, the kinematics equations were derived based on the D—H method. The kinematics simulation of the manipulator was conducted using Matlab Robotics Toolbox, the simulation results showed that the kinematics analysis was entirely correct. Based on these, the manipulator physical prototype was manufactured, and the manipulator kinematics and end-effectors picking experiments were carried out under laboratory environment. The results showed that the picking operation strategy was reasonable and feasible, the position error of manipulator end was less than 9mm, and the picking success rate could reach 82.14%.