Heavy-ion (HI) irradiation is a unique approach to induce defects in semiconductor films. The ion irradiation leaves continuous columnar tracks to create various defects and reduce film density, modulating the thermoelectric properties of semiconductor films. As a p-type transparent oxide semiconductor (TOS), the as-synthesized CuAlO2 films were irradiated with different doses of Fe10+ ions at room temperature using the 320 kV High Voltage Platform, and then post-annealed to improve the microstructure and thermoelectric properties. The irradiated CuAlO2 films, with 15 × 1013 ions cm−2, can achieve an electrical conductivity of 0.14 S cm−1, which is about 200 times larger than the unirradiated counterparts. The Seebeck coefficient reaches up to 189.80 and 208.58 μV K−1 at room temperature and 600 K, respectively. Therefore, a high power factor (PF) of 9.15 μW m−1K−2 is rendered by the irradiated CuAlO2 films, whereas the unirradiated films are not detected in the given measurement range. The improved thermoelectric performance is mainly due to the increased copper vacancies in irradiated films without significantly reducing the crystallinity. The current work presents a promising strategy to improve the thermoelectric performance of semiconductor films.