Taking the attitude control system of micro quad-rotor as a research object, a design scheme of fault estimator based on generalized Kalman-Yakubovic-Popov (GKYP) lemma is put forward to deal with the problem of estimating multiple actuators malfunctions with couplings. Using an H_index and an appropriate algorithm, the goal of weakening the coupling can be achieved by limiting the fault frequency to a certain range, then different kinds of actuator faults can be estimated correctly. The simulations demonstrate the reliability and validity of the proposed method.