The Chinese Chang’E-4 mission for moon exploration has been successfully completed. The Chang’E-4 probe achieved the first-ever soft landing on the floor of Von Kármán crater (177.59°E, 45.46°S) of the South Pole-Aitken (SPA) basin on January 3, 2019. Yutu-2 rover is mounted with several scientific instruments including a lunar penetrating radar (LPR), which is an effective instrument to detect the lunar subsurface structure. During the interpretation of LPR data, subsurface velocity of electromagnetic waves is a vital parameter necessary for stratigraphic division and computing other properties. However, the methods in previous research on Chang’E-3 cannot perform velocity analysis automatically and objectively. In this paper, the 3D velocity spectrum is applied to property analysis of LPR data from Chang’E-4. The result shows that 3D velocity spectrum can automatically search for hyperbolas; the maximum value at velocity axis with a soft threshold function can provide the horizontal position, two-way reflected time and velocity of each hyperbola; the average maximum relative error of velocity is estimated to be 7.99%. Based on the estimated velocities of 30 hyperbolas, the structures of subsurface properties are obtained, including velocity, relative permittivity, density, and content of FeO and TiO2.