In the fabrication processes of thin film thermoelectrics, a subsequent annealing treatment is inevitable to reduce the defects and residual stresses introduced during the film growth, and to make the uniform carrier concentration of the film. However, the diffusion-induced atomic redistribution and the broadening of p/n junction region are expected to affect the thermoelectric properties of thin film modules. The present study intends to investigate the diffusion at the p/n junctions of thermoelectric thin films and to relate it to the property changes. The film junctions of p-type(Bi0.5Sb1.5Te3)and n-type(Bi2Te2.4Se0.6)were prepared by the flash evaporation method. Aluminum thin layer was employed as a diffusion barrier between p-and n-type films of the junction. This was found to be an effective barrier by showing a negligible diffusion into both type films. After annealing treatment, the thermoelectric properties of p/n couples with aluminum barrier layer were accordingly retained their properties without any deterioration.