The configuration boundedness of the three-body model dynamics is studied for Sun-Earth formation flying missions. The three-body formation flying model is built up with considering the lunar gravitational acceleration and solar radiation pressure. Because traditional linearized dynamics based method has relatively lower accuracy, a modified nonlinear formation configuration analysis method is proposed in this paper. Comparative studies are carried out from three aspects, i.e., natural formation configuration with arbitrary departure time, initialization time and formation configuration boundedness, and specific initialization time for bounded formation configuration. Simulations demonstrate the differences between the two schemes, and indicate that the nonlinear dynamic method reduces the error caused by the model linearization and disturbance approximation, and thus provides higher accuracy for boundedness analysis, which is of value to initial parameters selection for natural three-body formation flying.