In contrast to previous findings, a high-temperature phase Li4.1Si, rather than the commercial phase Li15Si4, was observed in the hollow-structured silicon anode of a Li-ions battery after lithiation. The formation of Li4.1Si, as well as other lithium silicides, could be ascribed by the polymorphic transition theory that promoted the formation of a metastable phase. The phase transition began with a nucleus composed of a specific octahedral, which led to the final phases containing similar short-range ordering. Due to the formation of the Li4.1Si, the hollow-structured silicon anode had an ultra-high capacity that remained at 2500 mAh/g after 250 cycles. This kind of phase transition may occur not only in hollow-structured silicon nanoparticles but also in other particles with specific morphologies if the requirements for polymorphic transition are satisfied.