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Abstract Grain-boundary atomic structures of crystalline materials have long been believed to be commensurate with the crystal periodicity of the adjacent crystals. In the present study, we experimentally observed a Σ9 grain-boundary atomic structure of a bcc crystal (Fe-3%Si). It is found that the Σ9 grain-boundary structure is largely reconstructed and forms a dense packing of icosahedral clusters in its core. Combining with the detailed theoretical calculations, the Σ9 grain-boundary atomic structure is discovered to be incommensurate with the adjacent crystal structures. The present findings shed new light on the study of stable grain-boundary atomic structures in crystalline materials.