Thermoelectric properties of metal chalcogenide based materials exhibit a great suitability in the field of energy sustainability. This study reports the thermoelectric properties of In2(Te0.94Se0.06)3films prepared by thermal evaporation before and after the electronic excitations produced by 120 MeV Au ions. The Seebeck coefficient value for pristine sample is found to be ~196 µV K−1 and it is enhanced to ~347 µV K−1 at the higher fluence of 1 × 1013 ions/cm2 at 400 K. The negative value of Seebeck coefficient and the Hall effect measurements confirm the n-type conductivity in the pristine and irradiated samples. The power factor value of thin films irradiated at the fluence of 1 × 1013 ions/cm2 is ~3.80 μW/K2 m, as compared to pristine sample ~1.28 μW/K2 m. The change in image contrast in FESEM is due to grain fragmentation with increase in ion fluence in comparison to the pristine sample. It is evident that the electrical resistivity and power factor values are higher for irradiated samples as compared to that of pristine samples. Moreover, presence of high density of nanoscale grain boundaries created by ion irradiations lead to the enhancement in thermoelectric properties of In2(Te0.94Se0.06)3 thin films.