The relations between the morphology and electrochemical performance of the thin film anodes made of copper and silicon are investigated. A well-aligned nanorods containing composite thin film and a composite thin film with no alignment in its structure are fabricated by electron beam deposition. Galvanostatic half-cell measurements show that the well-aligned anode exhibits a longer cycle life with a moderate capacity due the particularities in its composition, structure and morphology: Cu in the films buffers the mechanical stress occurred during lithiation and the existence of amorphous and nano-sized particles enhances cycleability. Moreover, the nanorods formation in the thin film increases the contact area of the anode with Li and decreases the polarization on the electrode surface. Plus, the homogenously distributed nano-sized interspaces among these nanorods enhance the mechanical tolerance of the electrode against volumetric changes.