Owing to the earth-abundancy, eco-friendliness and high thermoelectric performance, CoSb3 skutterudites have been employed in thermoelectric devices with a high energy conversion efficiency. However, the thermoelectric performance of CoSb3-based thin films is still relatively low within the medium temperature range. In this work, we report a record high ZT of ~0.65 at 623 K in the n-type Ag/In co-doped CoSb3 thin films, fabricated by a facile magnetron sputtering technique. Extensive characterizations and computational results indicate both Ag and In as fillers prefer to occupy the interstitial sites in the CoSb3 lattice. A 0.2% Ag doping induces impurity states in the band structure of CoSb3, boosts the density-of-states near the Fermi level and enhances the absolute Seebeck coefficient up to ~198 μV K−1. Simultaneously, a 4.2% In doping further tunes the bandgap, increases the electrical conductivity up to ~75 S cm−1, and contributes to an optimized power factor of ~2.94 μW cm−1 K−2 at 623 K. In addition, these interstitial dopants accompanying with dense grain boundaries contribute an ultra-low thermal conductivity of ~0.28 W m−1 K−1 at 623 K, leading to a high ZT in the film system. This work demonstrates that rational band engineering and structural manipulations can achieve high performance in n-type CoSb3-based thin films, which possess full potential for applying to miniature thermoelectric devices.