Au films are deposited on fused silica substrates using the magnetron sputtering technique. The phase structure and surface morphology of the Au film after femtosecond pulse laser irradiation near laser induced damage threshold (LIDT) are investigated. The results show that the Au film prepared by magnetron sputtering is (111) oriented growth film. Laser irradiation energy near LIDT causes Au film to form large grains in the irradiated area and become polycrystalline structure from (111) single orientation. The increase of grain size leads to the increase of surface roughness. The experimental results provide a certain basis for exploring the damage process and later application of Au film under femtosecond laser.