The technological advances in wearable electronics and military stealth have spawned extensive research into electromagnetic wave absorbents. Despite the rapid progress in the geometrical modulation of magnetic absorbents, the engineering strategy of microwave-responsive magnetic domains is underdeveloped and the response dynamics remain unclear. Herein, a surface finite-sized atom reconstruction procedure is proposed to accurately modulate the local magnetic topological domains, dramatically enhancing the magnetic loss capacity. Due to the selectivity of atom reconstruction, vortex and stripe domains are controllably hybridized around the porous surface to broaden the interactive domain region, significantly intensifying energy absorption of the microwave field. Meanwhile, the amorphous/crystalline interfaces around atom reconstruction regions can induce interfacial polarization, enabling the optimization of dielectric loss capacity. Therefore, a satisfactory magnetic–dielectric synergy is realized to demonstrate the strong absorption intensity of −31.2 dB and the broad absorption bandwidth of 5.9 GHz. Furthermore, the surface-based magnetic domain transformation and microwave energy attenuation mechanisms are thoroughly revealed to break the black box of structure–function through electron holography and micromagnetic simulation. These achievements demonstrate a promising solution to improve high-frequency magnetic properties and provide a feasible route to interpret the structure-relevant magnetic loss capacity.