The flexible manipulator is widely used in the fields of nuclear industry, construction industry, space exploration and so on, but because of its characteristics of low stiffness, large deflection and low damping, the end of the vibration is difficult to eliminate in a short time. In this paper, a method of vibration reduction trajectory planning for the hybrid structure flexible manipulator with a rotating joint and a telescopic joint is studied. The dynamic and kinematic models are established by the structural decomposition and rigid flexible partial decomposition. In order to improve the efficiency of the algorithm, the weighted factor is introduced and the mapping function is constructed to select the non-uniform interpolation point. The interpolation point position increment is optimized by using the particle swarm optimization algorithm(PSO), and a new trajectory function is fitted by three spline interpolation. Finally, the effectiveness of the proposed method is verified by designing a control system of the hybrid flexible manipulator.