Poor cyclability and rate performance are two key problems hindering the practical application of In2O3 in high power lithium-ion batteries. Herein, we report a phase transition strategy to fabricate novel In1- xZnxOy heterogeneous nanofibers with mixed phases of cubic bixbyite-type In2O3 and rhombohedral corundunm-type In2O3 to enhance the lithium ion storage ability. The one-dimensional structure shortens the path for lithium ion diffusion and electron transfer, and accommodates the large volume changes upon cycling. The introduction of rhombohedral corundunm-type In2O3 can favorably improve the electrical conductivity, provide more pathways for lithium ion diffusion, and optimize the interface interplay. The optimal In0.5Zn0.5O1.25 heterogeneous nanofibers exhibit superior cyclic stability and outstanding high-rate performance, which can be ascribed to the synergistic effects of excellent electrical conductivity, more pathways for lithium ion diffusion, and the coupling effect of heterogeneous interface. This new phase-transition induced formation of heterostructure nanofibers is enlightening in design high performance electrode materials for lithium ion batteries.