Abstract Magnetic ordering modulation is essential for enhancing the functionality of materials and devices. However, achieving precise control over the orientation and positioning of magnets within nanostructures through spatial manipulation remains a significant challenge due to the magnetic self‐aggregation. Herein, a strategy is proposed to quantitatively regulate the viscous forces acting on particles within a spray stream under an applied electric field, modifying the kinetic energy to customize the spatial distribution. Notably, this is a general approach applicable to particles of various sizes and shapes, including cubes, spheres, ellipses, peanut‐shaped, ranging from tens of nanometers to several microns. Micromagnetic simulations validate the nanoscale spacing of magnetic units and the corresponding magnetic interactions, providing new insights into the relationship between spatial distribution and magnetic loss. The magnetic exchange coupling between the well‐aligned ferromagnetic cubes in the Fe‐3@C@Fe tube results in a prominent multifold enhancement of saturation magnetization intensity, with the permeability substantially increasing by two orders of magnitude, particularly at high frequencies. Meanwhile, the abundant heterogeneous interfaces trigger polarization effects, which synergistically facilitate an improved electromagnetic absorption ability. This work opens new avenues for creating complex superstructures with unique magnetic functionalities for advanced materials and devices.