Single crystalline metal oxide nanowires formed via a vapor-liquid-solid (VLS) route provide a platform not only for studying fundamental nanoscale properties but also for exploring novel device applications. Although the crystal phase variation of metal oxides, which exhibits a variety of physical properties, is an interesting feature compared with conventional semiconductors, it has been difficult to control the crystal phase of metal oxides during the VLS nanowire growth. Here we show that a material flux critically determines the crystal phase of indium-tin oxide nanowires grown via the VLS route, although thermodynamical parameters, such as temperature and pressure, were previously believed to determine the crystal phase. The crystal phases of indium-tin oxide nanowires varied from the rutile structures (SnO2), the metastable fluorite structures (InxSnyO3.5) and the bixbyite structures (Sn-doped In2O3) when only the material flux was varied within an order of magnitude. This trend can be interpreted in terms of the material flux dependence of crystal phases (rutile SnO2 and bixbyite In2O3) on the critical nucleation at the liquid-solid (LS) interface. Thus, precisely controlling the material flux, which has been underestimated for VLS nanowire growths, allows us to design the crystal phase and properties in the VLS nanowire growth of multicomponent metal oxides.