Ag thin films having attractive optical transmittance and effective shielding capability are usually used as a preferred choice for the transparent electromagnetic shielding windows. Whereas, the Ag films are grown primarily via an island growth (Volmer-Weber) mechanism, which greatly restricts its application. In this study, by introducing Al atoms and suitable annealing treatment, the continuous and smooth Ag thin films are successfully fabricated by magnetron co-sputtering method. The effect of annealing temperature on the microstructure, optical and electromagnetic shielding properties of the films are conducted the comprehensive and profound study. Our results indicate that the 5 mol% Al-Ag thin film annealed at 200 °C could transform into planar growth structure, and display excellent the highest optical transmittance 89.15% at 550 nm. Meanwhile, the shielding effectiveness (SE) reaches a peak value of 28.1 dB. 500°C is estimated as the threshold annealing temperature of Al-Ag thin film with comprehensive performances gradually declining. Moreover, the Al dopants significantly improve the thermal stability of Ag thin films than that of the pure Ag films. These findings are of important guidance for the preparation of high-quality Al-Ag thin films to meet the practical applications.