Evolution of the chemical bonding nature and electrochemical activity of indium selenide upon the composite formation with carbon species is systematically investigated. Nanocomposites of In4Se2.85@graphene and In4Se2.85@carbon-black are synthesized via a solid state reaction between In and Se elements, and the following high energy mechanical milling of In4Se2.85 with graphene and carbon-black, respectively. The high energy mechanical milling (HEMM) of In4Se2.85 with carbon species gives rise to a decrease of particle size with a significant depression of the crystallinity of In4Se2.85 phase. In contrast to the composite formation with carbon-black, that with graphene induces a notable decrease of (InSe) bond covalency, underscoring significant chemical interaction between graphene and In4Se2.85. Both the nanocomposites of In4Se2.85@graphene and In4Se2.85@carbon-black show much better anode performance for lithium ion batteries with larger discharge capacity and better cyclability than does the pristine In4Se2.85 material, indicating the beneficial effect of composite formation on the electrochemical activity of indium selenide. Between the present nanocomposites, the electrode performance of the In4Se2.85@graphene nanocomposite is superior to that of the In4Se2.85@carbon-black nanocomposite, which is attributable to the weakening of (InSe) bonds upon the composite formation with graphene as well as to the better mixing between In4Se2.85 and graphene. The present study clearly demonstrates that the composite formation with graphene has strong influence on the chemical bonds and electrode activity of indium selenide and the HEMM process with graphene nanosheet is fairly useful in exploring excellent electrode materials of metal chalcogenide–carbon nanocomposite for lithium ion batteries.