In this work, a novel hexagonal Li2MgSi anode is successfully prepared through a hydrogen-driven chemical reaction technique. Electrochemical tests indicate significantly improved cycling stability for the as-synthesized Li2MgSi compared with that of Mg2Si. Ball-milling treatment induces a polymorphic transformation of Li2MgSi from a hexagonal structure to a cubic structure, suggesting that the cubic Li2MgSi is a metastable phase. The post-24-h-milled Li2MgSi delivers a maximum capacity of 807.8 mAh g−1, which is much higher than that of pristine Li2MgSi. In particular, the post-24-h-milled Li2MgSi retains 50% of its capacity after 100 cycles, which is superior to cycling stability of Mg2Si. XRD analyses correlated with CV measurements do not demonstrate the dissociation of metallic Mg and/or Li–Mg alloy involved in the lithiation of Mg2Si for the Li2MgSi anode, which contributes to the improved lithium storage performance of the Li2MgSi anode. The findings presented in this work are very useful for the design and synthesis of novel intermetallic compounds for lithium storage as anode materials of Li-ion batteries.