Recently it has been demonstrated that the electrochemical performances of semiconducting amorphous anodes for Li-ion batteries (LIBs) can be greatly enhanced by the discharging/charging induced nanocrystals. However, the structural origin of those nano-domains remains elusive, although it is critically important for designing superior glass anodes for LIBs. In this work, we probe the local structural evolution in a glass anode for LIBs during cycles by means of the state-of-the-art solid-state nuclear magnetic resonance (SSNMR). The structural evolution is manifested as the disassociation of the structural network into isolated units, followed by formation of different types of nano-domains with a high degree of order. These domains are highly favorable for rate capability and long-term cycling stability. From SSNMR and electrochemical characterizations, we have obtained a clear picture about the detailed redox reactions. These findings provide a chemical principle that is helpful for designing the stable glass electrodes for high-performance LiBs.