Intrinsically conductive polymers have attracted much attention in the electromagnetic interference (EMI) shielding field because of their high conductivity and favorable flexibility. Delocalized π-electrons migrating along the conjugated long-chain structures can form a current. Based on this special conductive mechanism, the doping process significantly influences the conductivity and EMI shielding efficiency (SE). However, it is challenging to investigate the influence of the doping process on EMI shielding performance, which would enable the optimization of dopant selection. In this study, dopant engineering was explored for controllable conductivity, EMI SE, and mechanical properties. Polypyrrole (PPy) doped with various dopants serves as a conductive coating owing to its adjustable conductivity and abundant functional groups. Elastic thermoplastic polyurethane was chosen as the porous framework because of its high tensile strength, and magnetic nanoparticles supplied the magnetic loss in the 3D network. Eventually, the composite film showed the best properties when PPy was doped with sodium ptoluenesulfonate. The film exhibited an average SE of 26.3 dB in the X band and a specific SE of 1563.17 dB cm 2 g −1 with a thickness of merely 0.2 mm. This film withstood a tensile stress of 16.0 MPa, while the breaking elongation ratio reached 538.0%. After 10,000 cyclic bending, 92.3% of the EMI shielding property was retained. In summary, this study highlights the most suitable dopant for EMI shielding applications and provides a prospective alternative for advanced, flexible, and smart devices.