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Abstract We find a new relation between the spectral problem for Bloch electrons on a two-dimensional honeycomb lattice in a uniform magnetic field and that for quantum geometry of a toric Calabi-Yau threefold. We show that a difference equation for the Bloch electron is identical to a quantum mirror curve of the Calabi-Yau threefold. As an application, we show that bandwidths of the electron spectra in the weak magnetic flux regime are systematically calculated by the topological string free energies at conifold singular points in the Nekrasov-Shatashvili limit.