A feedforward approach for generating near time optimal controller for flexible spacecraft rest-to-rest maneuvers is presented with the objective insensitivity to modeling errors, parameter uncertainty and minimizing the residual energy of the flexible modes. The perturbation estimation of flexible appendages to the rigid-hub is accomplished simply via compare the output of real plant with the reference model, and the approach is based on combine this estimation with the bang-bang control for the rigid-hub modes through analysis the basic constraint and the additional constraint, i.e. zero coupling torque and zero coupling torque derivative for general two orders system and three orders system with considerate attitude acceleration mode near time optimal controls. These time optimal controls with control constraints and state constraints leads to forming a boundary- value problem, and resolved the problem using an iterative numerical algorithm.The near time optimal control with perturbation estimation shows a good robust to parameter uncertainty and can suppress the vibration and minimizing the residual energy. The capability of this approach is demonstrated through a numerical example in detail.