As models calculated by dynamic coefficients are constrained by small disturbance assumption, a new method of identifying missile body models is proposed. This method is based on Hartley modulating functions and Least Squares. According to the response for several kinds of signal, the transfer functions of an anti tank missile are identified in roll and pitch channels and are later validated by 6-degree-of-freedom trajectory simulation model. The results show that models obtained by the new method are more accurate than that calculated by dynamic coefficients, and are not constrained by small disturbance assumption. This method can be widely used in axial symmetric missiles.