In this work, a facile sequential electrochemical synthesis strategy is employed for the precisely controlled in situ polymerization of pyrrole on an iron oxide substrate in the oxalic acid system. The use of porous iron oxide as a template allows for the modification of polypyrrole to create a large conductive network while preserving the integrity of the substrate. This process improves the poor conductivity of conventional metal oxides, allowing for the synthesis of a Fe3O4/PPY hybrid electrode material. The experiments elucidated the mechanism of pyrrole surface morphology coupled with the deposition amount threshold affecting the electrode performance. This was achieved by elucidating the regulation laws of key deposition process parameters (pyrrole monomer concentration, scanning rate, and number of cycles) on the diffusion and oxidation behaviors of pyrrole during the continuous polymerization process. Furthermore, the electrochemical behaviors of the Fe3O4/PPY hybrid electrode were better resolved. The results demonstrate that the deposition amount of PPY on the Fe3O4/PPY hybrid electrode material is within the optimized threshold (1 × 10−6∼3 × 10−6 g), exhibiting a regular and uniform surface morphology with no agglomeration, which indicates a competitive specific capacitance (215.12 mF cm−2 at 1.1 mA cm−2). This strategy of structure-modulated synergistic functional hybridization offers a new approach for designing efficient binder-free hybridized electrode materials.