There has been a recent debate that boron nanotubes can outperform carbon nanotubes on many grounds. The most stable boron nanotubes are made of a hexagonal lattice with an extra atom added to some of the hexagons called ∝-boron nanotubes. Closed forms of M-polynomial of nanotubes produce closed forms of many degree-based topological indices which are numerical parameters of the structure and determine physico-chemical properties of the concerned nanotubes. In this article, we compute and analyze many topological indices of ∝-boron nanotubes correlating with the size of structure of these tubes through the use of M-polynomial. More importantly we make a graph-theoretic comparison of indices of two types of boron nanotubes namely triangular boron and ∝-boron nanotubes.