In order to improve the safety of hexanitrohexaazaisowurtzitane (CL-20), submicron CL-20 particles were prepared by a siphon ultrasonic-assisted spray refining experimental device. The samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), and differential scanning calorimetry (DSC), and the impact sensitivity of the samples was tested. The results show that the particle size of siphon-refined CL-20 is about 800 nm~1 μm, which is more smooth, mellow, and dense than that of CL-20 prepared by a traditional pressure-refined method. The peak diffraction angle of pressure- and siphon-refined CL-20 is basically the same as that of raw CL-20, and their crystal forms are ε type. The peak strength of pressure- and siphon-refined CL-20 decreased obviously. The apparent activation energy of pressure-refined CL-20 and siphon-refined CL-20 is 13.3 kJ/mol and 11.95 kJ/mol higher than that of raw CL-20, respectively. The thermal stability of CL-20 is improved. The activation enthalpy (ΔH#) is significantly higher than that of raw CL-20, and the characteristic drop is 70.4% and 82.7% higher than that of raw CL-20. The impact sensitivity of siphon-refined CL-20 is lower than that of pressure-refined CL-20, so the safety performance of an explosive is improved obviously.