Connected and airbag isolated Si-Ge nanorod (NR) arrays in different configurations have been fabricated on wafer scale Si substrates as anodes in micro-lithium ion batteries (LIBs), and the impacts of configurations on electrochemical properties of the electrodes were investigated experimentally and theoretically. It is demonstrated that the Si inner cores can be effectively protected by the connected Ge shells and contribute to the enhanced capacity by ∼68%, derived from an activation process along with the amorphization of the crystalline lattice. The first-principles calculations further verify the smaller forces on the Si layers at the atomic level during the restricted volume expansion with the covering of Ge layers. This work provides general guidelines for designing other composites and core-shell configurations in electrodes of micro-LIBs to accomplish higher capacities and longer cycle lives.