It is significant to efficiently and accurately determine the flutter boundary of various aircraft configurations in the aircraft design. In this paper, adopt the linear unsteady aerodynamic method and nonlinear unsteady aerodynamic method for the subsonic and transonic areas, respectively. The nonlinear method uses the transonic small disturbance equation based on the accuracy steady CFD results as inputs. All the flutter solutions use g method for different Mach areas. The flutter analysis is used for an beam and reduced stiffness FEM model of the whole aircraft including empty aircraft and three special fuel cases for choosing the typical altitudes and Mach number covering the flight envelope and determine the flutter envelopes for the four aircraft configuration. The flutter boundary of the aircraft is consistent with flight flutter test. Compared with other analysis methods, the efficiency is obviously improved, especially for a variety of aircraft configurations. Therefore, the method adopted in this paper is an efficient and accurate method for predicting flutter boundary of large aircraft, which is suitable for engineering at present.