Fe and Ni Kα X‐ray fluorescence holography measurements were conducted on a single crystal Fe65Ni35 Invar alloy at 100 and 300 K to investigate the temperature dependence of the 3‐dimensional local structures around the Fe and Ni atoms, respectively. Local structural information was obtained by detailed analyses using a L1‐regularized linear regression for the experimental data. At 100 K, the local atomic arrangements around both the elements show fcc structures. At 300 K, however, only the image around Fe shows a bcc‐like neighboring arrangement. From these X‐ray fluorescence holography data, we propose a model that with increasing temperature, an Fe atom with the low‐spin state enters at the central position of the fcc lattice and is stabilized. And then, large angular positional fluctuations are induced for the atoms at the face‐centered positions around the central Fe atom only.