In order to keep the stoichemistry of Bi2Te3 and Sb2Te3 so as to keep the electrical and thermal conductivity advantage of the layered structure of bulk Bi2Te3 and Sb2Te3 in each period of the superlattice, magnetron sputtering, which is operated at relatively low temperature, was used to deposit multiplayer Bi2Te3/Sb2Te3 thermoelectric superlattice device. The two guns in our magnetron sputtering device is oriented at a certain angle to get off-axis plasma plume, which will form lattice with preferential orientation for electrical conductivity in each layer. The super lattice was then bombarded by MeV Si ions with different fluence in order to form nanoscale cluster quantum dot-like structures. In addition to the effect of quantum well confinement of the phonon transmission, the nanoscale clusters produced by the bombardment of ion beam further adversely affect the thermal conductivity. The defect and disorder in the lattice caused by bombardment and the grain boundary of these nanoscale clusters increase the scattering of phonon and increase the chance of the inelastic interaction of phonon and the annihilation of phonon, this limits phonon mean free path. Phonons are chiefly absorbed and dissipated along the lattice, therefore reduces the cross plane thermal conductivity, The increases of the electron density of state in the miniband of nanoscale cluster quantum dot-like structure formed by bombardment also increases Seebeck coefficient, and the electrical conductivity. Eventually, the thermo-electric figure of merit of superlattice films increases.