The in situ synthesis of mesoporous nanotubes from natural minerals remains a great challenge. Herein, we report the successful synthesis of mesoporous silica nanotubes （MNTs） with a varying inner-shell thickness and a preserved clay outer shell from natural-halloysite nanotubes （HNTs）. After the enlargement of the lumen diameter of the tubular aluminosilicate clay by acid leaching, uniform mesopores were introduced by a modified pseudomorphic transformation approach, while the clay outer shell was well-preserved. Using density functional theory calculations, the atomic structure evolution and the energetics during A1 leaching and Si-OH condensation were studied in detail. After the leaching of A1 ions from the HNTs, local structural changes from Al（Oh） to A1（V） at a medium leaching level and to AI（Td） at a high leaching level were confirmed. The calculated hydroxylation energy of two kinds of silica components in the acid-leached HNTs （the distorted two-dimensional silica source in the inner shell and the intact aluminosilicate structure in the outer shell） was 0.5 eV lower or 1.0 eV higher than that of bulk silica, which clarifies the different behavior of the silica components in the hydrothermal process. The successful synthesis of reactive MNTs from HNTs introduces a new strategy for the synthesis of mesoporous nanocontainers with a special morphology using natural minerals. In particular, MNT samples with numerous reactive AI（V） species and a specific surface area up to 583 m^2/g （increased by a factor of 10） are promising drugloading nanocontainers and nanoreactors.