Oxygen vacancies (OVs) are reported for the first time as an effective strategy to boost the electrochemical performance for amorphous electrode materials of sodium-ion batteries (SIB). Amorphous SnO2 is used as a model anode material to demonstrate the significant impact of OVs because it has received much attention in the SIB field. Amorphous SnO2 ordered arrays are fabricated using the nanoimprinted anodic aluminum oxide (AAO) template and atomic layer deposition and OVs are confined in the material by annealing the arrays in the N2 atmosphere. The OVs-containing amorphous SnO2 ordered arrays, used as binder- and conductive additive-free anodes, exhibit high reversible capacity and good cycle life by retaining the capacities of 376 mAh g−1 after 100 cycles at 0.05Ag−1 and 220 mAh g−1 after 800 cycles at 1Ag−1. They also show great rate capability by delivering the capacities of 210 and 200 mAh g−1 at 10 and 20Ag−1, respectively. Electrochemical kinetic study reveals that the presence of OVs greatly enhances charge transfer/transport in the amorphous SnO2, thereby boosts the performance comparing with the OVs-free counterpart. This work highlights the importance of modulating defects in amorphous electrode materials toward promoted sodium storage.