The residual vibration of the single-link flexible manipulator (SLFM) occurs during the point-to-point motion driven by the permanent magnet linear motor (PMLM)which can affect the rapid and precise location. To suppress the residual vibrationthe model identification of translational flexible manipulator system driven by PMLM is studied. The transfer function from position command to strain vibration at the root of the flexible manipulator is establishedand then the model is identified by step and frequency sweep input methodwhich lay the foundation for the control method of flexible manipulator system driven by PMLM to suppress the residual vibration. The experimental results show that the fitting ratios between the simulation output value of the identification model and the actual dynamic response of the PMLM SLFM system are both high. The results verify the model identification and also reflect the dynamic characteristics of the flexible manipulator system based on PMLM.