We investigate the structure stability, stretching, compressing, shearing, random shifting and X-ray diffraction of Ni based superconductive material EuNi2Si2 with different space group numbers based on inversed interatomic potentials obtained with Chen-Mbius lattice-inversion technique. It is found that the space group number of 139 has the lowest binding energy and the structure is the most stable. Furthermore, the phonon density and the thermodynamic properties of the stable structure are calculated and discussed. The phonon density of states shows that the low frequency range is dominated by the rare-earth element Eu with larger atomic mass. While with frequency increasing, the Si atoms with smaller atomic mass become more and more prominent. For the specific heat and the vibrational entropy, Eu and Ni contribute more in the low temperature range, Si becomes more and more prominent with temperature increasing.