Crystal structures of the multiferroic Eu1−xYxMnO3 (x = 0.2, 0.4) are investigated from the point of view of average and local structure analyses using single‐crystal X‐ray diffraction (XRD) and X‐ray fluorescence holography (XFH). With increasing Y content, the lattice constants decrease and the orthorhombic distortions increase. The differences between the local structures around Eu and Y are observed in the reconstructed atomic images by XFH. x = 0.2 and 0.4 compounds exhibit different local distortions at Mn sites, whereas no characteristic difference is shown in the average structures. In this system, the long‐range structural coherence is likely to be maintained even with significant substitution of Y.