Three-dimensional (3D) atomic images around the Tl atoms in single-crystal TlInSe₂ thermoelectric material in the incommensurate phase were reconstructed by Tl L _III X-ray fluorescence holography measured at room temperature. In the obtained 3D image, the In atoms are clearly visible at the proper positions in the normal phase. The Tl atomic images are also observed but very weakly. By comparing the experimental image with a theoretically calculated one, it is concluded that only the Tl atoms have large spatial fluctuations, which are related to the incommensurate phase of this material.