Aiming at the quantum radar cross section computational problems of missiles, a cone-pillared composite model is used to simulate the missile target geometry. The single-photon wave equation is introduced to derive and improve quantum radar cross section expressions. By interfering with the interaction of atoms and photons on the mirror surface, the intensity of the photons scattered by the target atoms is measured at the detection point to obtain the quantum radar cross section formula of the cone column compound target. The simulation results show that the mainlobe peak of single-photon quantum radar cross section is higher than that of classical radar cross section and the quantum radar cross section sidelobes peak is lower than that of classical radar cross section under different incident angles. The quantum radar cross section decreases with decreasing wavelength, and the incident angles have no influences on quantum radar cross section. It shows that the quantum radar has a high detection and identification ability for small targets and the resolution can reach nanometer level, which provides a basis for missile target identification.