In order to clarify a defensive party’s understanding of the threat of incoming hypersonic cruise missiles（HCMs） in near space and improve the existing missile defense strategy， the characteristics between HCM and cruise missile are compared and analyzed from the perspective of early warning system. By establishing target motion model， infrared detection model and radar detection model with moderate particle size， the influence of the cruising altitude and flying speed of the two kinds of targets on the ground-based early warning system and the infrared detectability are analyzed in detail and quantitatively. The results of comparative analysis show that the detection range of HCMs provided by the infrared detector is longer due to its stronger infrared radiation intensity. Although HCMs are faster than cruise missiles， the early warning time provided by the ground-based radar of HCMs with the same downrange is longer because of its higher altitude.