Graphene and its derivatives are widely used in the field of energy conversion and management due to their excellent physical and chemical properties. In this paper, ultra-thin graphite film (GF) with thickness of 100–150 nm prepared by chemical vapor deposition was transferred to oxygen plasma-treated polyimide (PI) substrate as flexible heating film. The electrothermal and photothermal properties of GF on PI substrates with different treatment time were studied. The experimental results show that the PI substrate pretreated by oxygen plasma can change the surface morphology of GF, increase its electrical conductivity and light absorption capacity, and significantly improve the electrothermal and photothermal properties of GF heater. Under the low applied voltage of 5 V (power density of 0.81 W cm−2), the surface temperature of GF on 40 min plasma-treated PI substrate can rise to 250 °C, which is nearly 50 °C higher than that of GF on untreated PI substrate. When 100 nm thick commercial multilayer graphene film (MLG) is used, plasma-treated PI substrate can increase the electric heating temperature of MLG by 70 °C. In terms of photothermal performance, the surface temperature of GF on 50 min plasma-treated PI substrate can reach 73 °C under one Sun irradiation, which is 8 °C higher than that on untreated substrate. The experimental results are in good agreement with the simulation research. Our strategy has important implications for the development of efficient and energy-saving graphene/graphite-based heating films for advanced electrothermal and photothermal conversion devices.