The stabilities of the gallium nanowires filled in carbon nanotubes (CNTs) have been studied using density functional theory (DFT). The results show that whether in CNTs or in free space, β-Ga nanowires with large sizes are more stable than α-Ga ones. By analyzing the average energies of gallium nanowires as well as the binding energies between gallium nanowires and CNTs, the reasons why not α-Ga but β-Ga is experimentally observed in CNTs are revealed.