A comprehensive method based on system identification theory for helicopter flight dynamics modeling with rotor degrees of freedom is developed. A fully parameterized rotor flapping equation for identification purpose is derived without using any theoretical model, so the confidence of the identified model is increased, and then the 6 degrees of freedom rigid body model is extended to 9 degrees of freedom high-order model. Bode sensitivity function is derived to increase the accuracy of frequency spectra calculation which influences the accuracy of model parameter identification. Then a frequency domain identification algorithm is established. Acceleration technique is developed furthermore to increase calculation efficiency, and the total identification time is reduced by more than 50% using this technique. A comprehensive two-step method is established for helicopter high-order flight dynamics model identification which increases the numerical stability of model identification compared with single step algorithm. Application of the developed method to identify the flight dynamics model of BO 105 helicopter based on flight test data is implemented. A comparative study between the high-order model and rigid body model is performed at last. The results show that the developed method can be used for helicopter high-order flight dynamics model identification with high accuracy as well as efficiency, and the advantage of identified high-order model is very obvious compared with low-order model. A comprehensive method based on system identification theory for helicopter flight dynamics modeling with rotor degrees of freedom was developed. A fully parameterized rotor flapping equation for identification purpose is derived without using any theoretical model, so the confidence of the identified model is increased, and then the 6 degrees of freedom rigid body model is extended to 9 degrees of freedom high-order model. Bode sensitivity function is derived to increase the accuracy of frequency spectra calculation which influences the accuracy of model parameter identification. Then a frequency domain identification algorithm is established . Acceleration technique is developed furthermore to increase calculation efficiency, and the total identification time is reduced by more than 50% using this technique. A comprehensive two-step method is established for helicopter high-order flight dynamics model identification which increases the numerical stability model identification compar ed with single step algorithm. Application of the developed method to identify the flight dynamics model of BO 105 helicopter based on flight test data is implemented. A comparative study between the high-order model and rigid body model is performed at last. The results show that the developed method can be used for helicopter high-order flight dynamics model identification with high accuracy as well as efficiency, and the advantage of identified high-order model is very obvious compared with low-order model.