Polymer nanocomposites incorporating inorganic nanofillers have emerged as highly promising electromagnetic interference (EMI) shielding materials, combining mechanical compliance with robust conductive percolation networks. Carbon nanotubes (CNTs) are particularly attractive as conductive fillers because their high aspect ratio facilitates percolation at low loadings. Also, CNTs offer superior mechanical durability under deformation compared to rigid, fracture-prone metal nanowires. For EMI shielding, high electrical conductivity is critical as it enhances both reflection and absorption through efficient charge dissipation and conduction losses. However, achieving highly aligned conductive pathways without degrading the intrinsic electrical properties of CNTs remains a significant challenge. Here, we demonstrate a non-destructive magnetic surface-functionalization and alignment strategy. Using a polydopamine (PDA)-mediated route, pristine multiwalled CNTs are uniformly decorated with Fe₃O₄ nanoparticles (FMWCNTs). This enables highly effective magnetic field-driven alignment at fields as low as 10 mT, promoting the strategic formation of percolation networks. By optimizing the Fe₃O₄/MWCNT ratio for high saturation magnetization and uniform coverage, the aligned FMWCNTs exhibit significant electrical anisotropy, delivering a 10.7-fold higher electrical conductivity in the parallel configuration compared to the vertical configuration. These findings present a scalable, room-temperature platform for engineering directionally enhanced conductivity in polymer nanocomposites, with broad applicability in advanced EMI shielding, flexible electronics, and advanced packaging technologies.