The quaternary compound Cu2ZnSnSe4 (CZTSe), as a typical candidate for both solar cells and thermoelectrics, is of great interest for energy harvesting applications. Materials with a high thermoelectric efficiency have a relatively low thermal conductivity, which is closely related to their chemical bonding and lattice dynamics. Therefore, it is essential to investigate the lattice dynamics of materials to further improve their thermoelectric efficiency. Here we report a lattice dynamic study in a cobalt-substituted CZTSe system using temperature-dependent X-ray absorption fine structure spectroscopy (TXAFS). The lattice contribution to the thermal conductivity is dominant, and its reduction is mainly ascribed to the increment of point defects after cobalt substitution. Furthermore, a lattice dynamic study shows that the Einstein temperature of atomic pairs is reduced after cobalt substitution, revealing that increasing local structure disorder and weakened bonding for each of the atomic pairs are achieved, which gives us a new perspective for understanding the behavior of lattice thermal conductivity.