We study a quantum information storage scheme based on an atomic ensemble with near (also exact) three-photon resonance electromagnetically induced transparency (EIT). Each 4-level-atom is coupled to two classical control fields and a quantum probe field. Quantum information is adiabatically stored in the associated dark polariton manifold. An intrinsic nontrivial topological structure is discovered in our quantum memory implemented through the symmetric collective atomic excitations with a hidden $\mathrm{SU}(3)$ dynamical symmetry. By adiabatically changing the Rabi frequencies of two classical control fields, the quantum state can be retrieved up to a non-Abelian holonomy and thus decoded from the final state in a purely geometric way.
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