In the past two decades, boron nanotubes have received significant attention from researchers and scientists due to their wide-ranging applications in electronics, nanodevices, optical engineering, nanobiotechnology, and cosmetics. These nanotubular structures composed of boron present exceptional electrical and mechanical properties, making them highly potential nanomaterials. In this article, we study the molecular structure of significant classes of boron nanotubes, namely, trihexagonal boron nanotubes, triangular boron nanotubes, and boron-α nanotubes. Furthermore, we calculate various topological indices for these nanotubes, including the augmented Zagreb index, Sombor index, reduced Sombor index, sum-connectivity index, and arithmetic–geometric index. These indices hold substantial importance in assessing the physical, chemical, and biological characteristics of boron nanotubes.