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NaYTl2 crystallizes in the orthorhombic Immm space group. The structure is one-dimensional and consists of two NaYTl2 ribbons oriented in the (1, 0, 0) direction. Na is bonded in a linear geometry to two equivalent Tl atoms. Both Na–Tl bond lengths are 3.14 Å. Y is bonded in a linear geometry to two equivalent Tl atoms. Both Y–Tl bond lengths are 3.11 Å. Tl is bonded in a linear geometry to one Na and one Y atom.
NaYTl2 is Heusler structured and crystallizes in the cubic Fm-3m space group. The structure is three-dimensional. Na is bonded in a body-centered cubic geometry to eight equivalent Tl atoms. All Na–Tl bond lengths are 3.30 Å. Y is bonded in a body-centered cubic geometry to eight equivalent Tl atoms. All Y–Tl bond lengths are 3.30 Å. Tl is bonded in a body-centered cubic geometry to four equivalent Na and four equivalent Y atoms.