Here, we report a tunable morphological transformation of indium oxide (IO) nanoflute, that is, nanowires embedded with discrete and hollow nanocavities to indium-filled IO nanotubes by simply controlling the In/O partial pressure in a thermal chemical vapor deposition method. The growth of nanoflute is observed as a prestage for the growth of indium-filled IO nanotubes. The outdiffusion of indium metal at lower In/O partial pressure results in the growth of discrete and hexagonal-shaped nanocavities enclosed by minimum surface energy planes, {111}, which get connected together for the formation of continuous and indium-filled IO nanotubes at higher In/O partial pressures. The tunable and controlled growth of indium-filled IO nanotubes may have potential applications in future nanodevices.