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We study the exciton condensate (EC) in a bilayer two-dimension-electron-gas (2DEG) adjacent to a type-II superconductor thin film with an array of pinned vortex lattices. By applying continuum low energy theory and carrying numerical simulations of lattice model within mean-field approximation, we find that if the order parameter of EC has a vortex profile, there are exact zero modes and associated \emph{rational} fractional charge for zero pseudospin potential () and average chemical potential (): =0 and =0; while for and =0, intervalley mixing splits the zero energy levels, and the system exhibits \emph{irrational} fractional \emph{axial} charge.

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