The residual vibrations in flexible structure system model can cause errors. In addition, the parameters in the system are also changed. For the problem of residual vibration, robust H∞ filter is designed for neutral systems with multi-delay. Based on Lyapunov stability theory, the sufficient condition for the existence of filter is given. For the permitted uncertainty and multi-delay, the designed filter can guarantee the robust asymptotically stability and satisfy H∞ performance index for the filtering error dynamic system. Finally, the designed filter is applied to the flexible system, and the result shows that the filter is effective.