Tip deflection and vibration have a large impact on the manipulator operation safety, and hybrid structure flexible manipulator has a larger workspace and more flexibility. In this paper, a new modeling scheme for a hybrid structure flexible manipulator is proposed. In the proposed scheme, the joint variables of hybrid structure flexible manipulator are divided in rigid joint angle and small joint angle deviations. The prismatic joint is divided into three segments according to the structure features of flexible manipulator. The three segments are the foundation segment, overlap segment and extension segment. Each segment is modeled by the theory of the Euler-Bernoulli beam, and the elastic deflection is described by assumed mode method, the kinetic energy and potential energy of every segment is analyzed respectively. Base on the previous researches of modeling for multi-link flexible manipulator, the dynamic equations of the manipulator are obtained by using the Lagrangian approach. In order to verify the correctness of model and analyze the characteristics of model, the comparative simulation experiments are designed. Tip vibration, angle deviation, vibration frequency and amplitude are observed, and the characteristics of the model are analyzed according to the experiment results.