To search the atomic sites of Mn impurities in Bi2Te3Mn0.1 topological insulator, a Mn Kα fluorescence x-ray holography experiment was performed. The reconstructed atomic image around the central Mn atom reveals a hexagonal configuration, where the local lattice constant is slightly larger than the original Bi2Te3 crystal. Thus, the most plausible atomic position of Mn impurities is the substitution with Bi or Te atom. The further-distant atomic images are hardly observed unlike usual crystals, indicating a formation of flat clusters around Mn in this functional crystal.