In this work, the initial configuration is first optimized by the first principle and interatomic pair potentials separately, the lattice parameters of the stable structure are in good agreement with the experimental values. The site preferences of La3Co29-xFexSi4B10 compounds are studied by using the first principle with density function theory method. The calculated results show that the substitution of Fe for Co has a strong preference for the 2c site, and the substitution sequence is 2c 8j1 8i2 8j2 8i3 16k 8i1, which is in good agreement with the experimental result The lattice parameters of La3Co29-xFexSi4B10 system change little, but the magnetic moment changes obviously, when only one Co atom is substituted by Fe atoms each time. We calculate the electronic densities of states and magnetic moments of La3Co29-xFexSi4B10 compound when all the Co atoms from different sites are substituted by Fe atoms with the preferential order With the increases of Fe content values in the La3Co29-xFexSi4B10, the curves of density of states move leftwards gradually. And the magnetic moment of the La3Fe29Si4B10 is larger than that of La3Co29Si4B10. Furthermore, the lattice vibrational and thermodynamic properties are predicted by using a series of interatomic pair potentials. The Co, Fe and La atoms contribute to the lower frequency vibrations because of their heavier mass. With the increase of Fe content the cut-off frequencies of La3Co29-xFexSi4B10 first decrease and then increase, and the vibration mode induced by Si element decreases in medium frequency. The very strong B-B interaction causes higher frequency vibrations. Furthermore, the specific heat, vibrational entropy and Debye temperature are predicted based on the phonon densities of states of the La3Co29-xFexSi4B10 with the different content values of Fe. The Debye temperature rises when the Fe content is bigger than Co content in La3Co29-xFexSi4B10compound.