We study the topological string partition function of a class of toric, double elliptically fibered Calabi-Yau threefolds X N;M at a generic point in the Kähler moduli space. These manifolds engineer little string theories in five dimensions or lower and are dual to stacks of M5-branes probing a transverse orbifold singularity. Using the refined topological vertex formalism, we explicitly calculate a generic building block which allows us to compute the topological string partition function of X N;M as a series expansion in different Kähler parameters. Using this result, we give further explicit proof for a duality found previously in the literature, which relates X N;M ∼ X N 0 ;M 0 for NM ¼ N 0 M 0 and gcdðN; MÞ ¼ gcdðN 0 ; M 0 Þ.