 For the first time, Si–Mo–O helices have been produced by the ion-assisted glancing angle electron beam co-evaporation of molybdenum oxide and silicon. Since the electron beam evaporation process forms metastable particles through the dissociation of the source material, a film that contains compounds of different combinations of molybdenum, silicon, and oxygen atoms is produced. This complex structure’s lithiation mechanism is different from that of the traditional electrodes in lithium-ion batteries. In the paper, the nanostructured Si–Mo–O anode was cycled in different potential windows (0.2–1.2 V, 0.2–3.0 V, 5 mV–3.0 V vs. lithium) at different rates. The anode remained cycling even at 0.7 mA cm−2, which makes it practical for micro- and solid-state battery applications. This research reveals that by adjusting the cutoff voltages, different particles could be activated in the anode structure to react with lithium, resulting in different performances. The electrode delivers higher capacity when cycled between 5 mV and 3.0 V windows and keeps cycling for 200 cycles under the load of 5 µA cm−2. This performance is believed to be related to the structural, morphological, and the compositional properties of the coating.