Conductive polymer composites have been utilized in the field of electromagnetic interference (EMI) shielding, albeit requiring a high concentration of conductive fillers to achieve desirable EMI performance. To address this issue and enable the creation of superior EMI shielding composites with reduced filler loadings, this study employed a pulsed magnetic field featuring an amplitude of 0.7 T, a pulse width of 10 μs, and a frequency of 100 Hz to align flaky carbonyl iron (FCI) in poly(dimethylsiloxane) (PDMS). This method resulted in an improved EMI shielding performance of the composites. The outcomes revealed that the pulsed magnetic field effectively controlled the orientation of the FCI, forming a conductive network structure, with the average orientation angle of the FCI reaching 69.3°. The aligned composites exhibited a significant improvement in EMI shielding effectiveness, with the enhancement effect reaching 37.53% and the EMI shielding effectiveness reaching 24.87 dB. Moreover, the flexible tensile properties of the aligned composites were superior to those of the unaligned composites, particularly the elongation at break, which reached 197.46%. The concordance between the theoretical analysis and experimental results affirms the efficacy of the microsecond pulsed magnetic field in enhancing the EMI shielding performance of composite materials. Ultimately, the high-performance, flexible electromagnetic shielding composite materials prepared in this study demonstrate potential for use in advanced electronic equipment.