The invention discloses an explosive substance testing system apparatus and testing method thereof. The apparatus includes an X-ray light path subsystem, a detecting subsystem, a servo subsystem and a computer subsystem, wherein the light path subsystem includes a 75Kev and a 150Kev energy segment white light sources; the light path subsystem and the detecting subsystem are totally mounted on a multiple shaft mechanical platform, at different angle positions at the same side relative to the object, so as to configure a Compton backscattering geometric light path. The testing method includes a computer software control method and a data processing method, including: adopting a control method integrating the scanning detecting and tracking detecting, acquiring the density information and Compton scattering energy difference pair information data of the object by a solid state detector to execute data-handling and characteristic matching, obtaining the density and effective atomic number information of the object, and determining whether the object is the explosive substance and the affiliated species by the pattern recognition, thereby implementing the quick, safe and nondestructive testing, which is suitable for flow ability test of case or human body carrying explosive substance.