Fatigue failure involves fatigue crack initiation and propagation processes. In bulk metals, the fatigue crack initiation process is strongly affected by a dissimilar surface layer, while the fatigue crack propagation process is less affected. In the case of the metallic thin films, which are a kind of small-scale metallic materials, have a large surface-area-to-volume ratio, and the fatigue crack propagation process is dominated by the formation of out-of-plane surface fatigue damage, intrusion/extrusion, which is observed in fatigue crack initiation process in bulk metals. Therefore, even a surface layer with a thickness on the order of nanometers would have a significant influence on fatigue crack propagation behavior of metallic thin films. In this study, in situ field emission scanning electron microscope (FESEM) observation experiments of fatigue crack propagation were conducted on freestanding copper thin films with a thickness of 500 nm with a thickness-controlled surface oxide layer in the range of ~0 nm to ~20 nm. The results showed that the fatigue crack propagation properties were influenced by the thickness of the surface oxide layer: acceleration of fatigue crack propagation, transitions of fatigue crack propagation mechanisms (from intrusion/extrusion mode to tensile-dominant mode) and unstable fracture occurred at smaller stress intensity factor range K for the films with a thicker surface oxide layer than that for the films with a thinner surface oxide layer. Moreover, the fatigue crack propagation rate da/dN was smaller in the region near the fatigue crack propagation threshold and thus the threshold stress intensity factor range Kth increased in the films with a thicker surface oxide layer. In situ FESEM observations showed that fatigue damage area around the fatigue crack became narrower in the films with thicker surface oxide layer, and the fatigue crack reached the threshold when intrusions/extrusions were rarely formed ahead of the crack tip. This suggests that the fatigue crack propagation threshold in metallic thin films is determined whether intrusions/extrusions are formed around the fatigue crack.