We report a facile and novel route to in-situ growth of conducting polypyrrole (PPy)/Fe3O4 nanocomposites via a counter-ion induced method, in which the cationic surfactant CTAB was used as a soft template, ammonium persulfate (APS) or FeCl3 was used as an oxidant, and organic acids were used as a configuration “directing” agent. The as-synthesized nanocomposites were characterized by TEM, XRD and the measurements of their electromagnetic properties. Experimental results show that both the kind of oxidant and the size of counter-ions in the polymerization system play the key roles in the fabrication of the morphologies of the final PPy/Fe3O4 nanocomposites. A uniform core-shell spherical nanostructure was formed when FeCl3 was used as the oxidant, whereas the string-bead nanostructure could be obtained when APS was used instead. The size of the counter-ions during the connection of micellar molecules could directly induce the formation of the PPy/Fe3O4 composites with various morphologies from spherical nanoparticles, nanofibers or string-bead nano-network to microtube structures. Meanwhile the loading amount of Fe3O4 ferrofluid would not only determine the diameter size of the string-bead nanostructures, but also the electromagnetic properties such as the microwave absorbing capacity of the resulting nanocomposites.