Organic electrode materials have long been proposed but their electrochemical performances are far from satisfactory in, for example, specific capacity and cycling stability, for secondary batteries. This article reports the electrochemical performance of a composite of polypyrrole (PPy) and nickel oxide (NiO), in which another lithium storage material, polypyrrole–nickel–oxygen (PPy–Ni–O) coordination complex, was fabricated during initial galvanostatically discharging. Extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations indicate the process of the electrochemical formation of a PPy–Ni–O coordination and determine its multilayer structure. The strong and electrochemically stable coordination between the nickel and nitrogen atoms ensures the excellent electrochemical performances of the complex. These findings pave new ways to construct a new type of high-performance organic anode material for lithium ion batteries.