To design and fabricate rational surface architecture of individual particles is one of the key factors that affect their magnetic properties and microwave absorption capability, which is still a great challenge. Herein, a series of Co₂₀Ni₈₀ hierarchical structures with different surface morphologies, including flower-, urchin-, ball-, and chain-like morphologies, were obtained using structure-directing templates via a facile one-step solvothermal treatment. The microwave reflection loss (RL) of urchin-like Co₂₀Ni₈₀ hierarchical structures reaches as high as −33.5 dB at 3 GHz, with almost twice the RL intensity of the ball- and chain-like structures, and the absorption bandwidth (<−10 dB) is about 5.5 GHz for the flower-like morphology, indicating that the surface nanospikes and nanoflakes on the Co₂₀Ni₈₀ microsphere surfaces have great influences on their magnetic microwave absorption properties. Electron holography analysis reveals that the surface nanospikes and nanoflakes could generate a high density of stray magnetic flux lines and contribute a large saturation magnetization (105.62 emu g⁻¹ for urchin-like and 96.41 emu g⁻¹ for flower-like morphology), leading the urchin-like and flower-like Co₂₀Ni₈₀ to possess stronger microwave RL compared with the ball-like and chain-like Co₂₀Ni₈₀ alloys. The eddy-current absorption mechanism μ′′(μ′)⁻²(f)⁻¹ is dominant in the frequency region above 8 GHz, implying that eddy-current loss is a vital factor for microwave RL in the high frequency range. It can be supposed from our findings that different surface morphologies of magnetic hierarchical structures might become an effective path to achieve high-performance microwave absorption for electromagnetic shielding and stealth camouflage applications.