The effects of cooling rate on the structure and magnetic properties of FePt films were studied. The results show that the in-plane coercivities of Fe53.6Pt46.4, Fe51.1Pt48.9 and Fe47.2Pt52.8 films in quenching and furnace cooling increased from 6.1 kOe to 7.0 kOe, 9.0 kOe to 12.0 kOe and 3.5 kOe to 8.8 kOe, respectively. The films in furnace cooling have continuous and uniform microstructure, and has good squareness of hysteresis loops. However, quenching cooling leads to island coalescence, forming a void morphology in the film. This study demonstrates that Fe dissolution and precipitation is greatly affected by cooling rate, and the magnetic properties and morphology of FePt films can be improved by controlling the cooling rate after heat treatment.