Abstract: Rational synthesis of nanowires via the vaporliquidsolid (VLS) mechanism with compositional and structural controls is vitally important for fabricating functional nanodevices from bottom up. Here, we show that branched indium tin oxide nanowires can be in situ seeded in vapor transport growth using tailored AuCu alloys as catalyst. Furthermore, we demonstrate that VLS synthesis gives unprecedented freedom to navigate the ternary InSnO phase diagram, and a rare and bulk-unstable cubic phase can be selectively stabilized in nanowires. The stabilized cubic fluorite phase possesses an unusual almost equimolar concentration of In and Sn, forming a defect-free epitaxial interface with the conventional bixbyite phase of tin-doped indium oxide that is the most employed transparent conducting oxide. This rational methodology of selecting phases and making abrupt axial heterojunctions in nanowires presents advantages over the conventional synthesis routes, promising novel composition-modulated nanomaterials.