In flight test, the measuring environment is very complexity. If the flight test data is unprocessed and directly used for the identification of aerodynamic derivatives, it will reduce the accuracy of the identification and even can result in iteration divergence or convergence to the error value. The paper puts forward a set of method, which contains identification and correction of data outliers, smoothing, filtering, time delay correcting, and compatibility checking, and the proposed flight test data processing method on the aerodynamic derivative identification accuracy effectively is verified by the flight test data.