The crystal internal defects of RDX/HMX were studied by optical microscopy with matching refractive(OMS), small angle scattering of X-ray(SASX),atomic force microscope(AFM), sink-fload method(SFM) and Mirco-CT. OMS and AFM results show that RDX/HMX has more defects and cracks than reduced sensitivity-RDX/reduced sensitivity-HMX. SASX results show that crystal internal defects of RDX/HMX are larger than that of RS-RDX/RS-HMX, and mirco-CT results show that RDX has larger internal defects than RS-RDX. Furthermore, shock sensitivity of RDX based PBXs and RS-RDX based PBXs were studied, and the results show that internal defects of RDX has great influence on shock sensitivity of RDX.