China Lead-based Research Reactor (CLEAR-I) will be built to develop the technologies of lead–bismuth eutectic cooled reactor. The In-Vessel Fuel Handling System (IVFHS) can achieve all positional refueling of the core by the complex operation of the double rotating plugs, the transfer machine and the rotor lift machine. One five degrees of freedom (5-DOF) rod mechanism of the IVFHS was proposed. Each joint parameter of the kinematic pairs was decided by the D-H method. The kinematics equation and velocity Jacobi matrix of the 5-DOF rod mechanism were deduced by the kinetic analysis. The rod position, rotation angle and velocity can be deduced by the moving trajectory of the transfer machine gripper. The feasibility was verified by the computer simulation and the principle prototype.