In recent years, there has been increasing interest in optoelectronic applications of transparent conductive oxide (TCO) thin-film-based materials and devices fabricated using patterning techniques. Meanwhile, femtosecond laser processing is a convenient method that further improves the performance of TCO-based functional devices and expands their application prospects. In this study, we proposed a simple and effective strategy to determine the fluences required for laser processing TCOs. We investigated the modification of an indium tin oxide (ITO) film induced by a femtosecond laser (45/150 fs, 800 nm) at different pulse fluences. The results reveal that the laser modification of ITO films is highly dependent on the irradiated pulse fluences. Several distinct types of final micro/nanostructures were observed and may be attributed to superficial amorphization, spallation ablation, stress-assisted delamination, boiling evaporation, and phase explosion. The final micro/nanostructures were studied in detail using optical microscopy, scanning electron microscopy, transmission electron microscopy and a surface profiler. At a lower fluence above the melting but below the ablation threshold, a laterally parabolic amorphous layer profiled with maximum thicknesses of several tens of nanometers was quantitatively attained. At a higher fluence, stress-assisted delamination and superheated liquid-induced micro-honeycomb structures emerged. Furthermore, the electron and lattice temperature evolutions were also obtained using a two-temperature model to prove the ablation mechanism and ascertain the micro/nanostructure formation principle. The predicted surface temperatures confirmed film amorphization without ablation below 0.23 J/cm2. These results reveal the interaction mechanism between femtosecond laser pulse and ITO film including the competition between the free electron heating of intraband transition and the multiphoton absorption of the interband transition, which promotes the potential applications for femtosecond laser processing TCO films and other wide-band-gap semiconductors such as photodetectors, solar cells, UV-light-emitting diodes, and flat-panel displays.