This paper considers model-free adaptive fault tolerant control of nonlinear system with measurement disturbance. Developing fault detection rule and reconfiguring controller and suppressing measurement disturbance’s impact are main focus points. Firstly, a model by using dynamic linearization technique is given. Secondly, to obtain the fault detection rule, a estimator is developed. And an online approximator is developed to acquire fault dynamics. Thirdly, an fault tolerant controller is reconstructed and then the stability analysis of proposed algorithm is given. As measurement disturbance influence tracking error, a modified model-free adaptive fault tolerant controller is utilized to decrease measurement disturbance. Finally, effectiveness is illustrated by simulations.