Abstract: The development of high-performance microwave absorption materials is one of the best strategies to combat electromagnetic wave radiation. Because of its large specific surface area, high magnetic saturation, and low coercivity, 2D flake carbonyl iron (FCI) is frequently employed in microwave absorption. However, its application prospects have been severely constrained by high specific gravity and excessive doping. In order to solve this problem, multiscale heterostructure (0D/1D/2D) Co@N Doped carbon nanotubes (NCNTs)/FCI nano-absorbent fillers were successfully constructed by combination FCI with 0D/1D Co@NCNTs composites with high electrical conductivity, large aspect ratio, and light weight. Finally, the flexible Co@NCNTs/FCI film were prepared by making full of the high flexibility of the polyurethane (PU) matrix. The Co@NCNTs/FCI nanocomposites demonstrate exceptional microwave absorption performance due to the dielectric/magnetic dual synergistic loss and the construction of multiscale heterostructure. At a filling ratio of 30 wt% and a thickness of 1.9 mm, the minimum reflection loss (RL_min) reaches −43.38 dB. Furthermore, because of the molecular thermal vibration of NCNTs and the localized surface plasmon resonance effect of Co nanoparticles, the Co@NCNTs/FCI film also exhibits remarkable photothermal conversion capabilities.