In chemical graph theory, a topological descriptor is a numerical quantity that is based on the chemical structure of underlying chemical compound. Topological indices play an important role in chemical graph theory especially in the quantitative structure-property relationship (QSPR) and quantitative structure-activity relationship (QSAR). In this paper, we present explicit formulae for some basic mathematical operations for the second hyper-Zagreb index of complement graph containing the join

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... G1 + G2, tensor product G1 \(\otimes\) G2, Cartesian product G1 x G2, composition G1 \(\circ\) G2, strong product G1 * G2, disjunction G1 V G2 and symmetric difference G1 \(\oplus\) G2. Moreover, we studied the second hyper-Zagreb index for some certain important physicochemical structures such as molecular complement graphs of V-Phenylenic Nanotube V PHX[q, p], V-Phenylenic Nanotorus V PHY [m, n] and Titania Nanotubes TiO2.