Zr2NiSe4 crystallizes in the monoclinic C2/m space group. Zr(1) is bonded to three equivalent Se(1) and three equivalent Se(2) atoms to form ZrSe6 octahedra that share corners with six equivalent Ni(1)Se6 octahedra, edges with six equivalent Zr(1)Se6 octahedra, and  a faceface with one Ni(1)Se6 octahedra. The corner-sharing octahedral tilt angles are 49°. Ni(1) is bonded to two equivalent Se(1) and four equivalent Se(2) atoms to form distorted NiSe6 octahedra that share corners with twelve equivalent Zr(1)Se6 octahedra, edges with two equivalent Ni(1)Se6 octahedra, and faces with two equivalent Zr(1)Se6 octahedra. The corner-sharing octahedral tilt angles are 49°. There are two inequivalent Se sites. In the first Se site, Se(1) is bonded in a rectangular see-saw-like geometry to three equivalent Zr(1) and one Ni(1) atom. In the second Se site, Se(2) is bonded to three equivalent Zr(1) and two equivalent Ni(1) atoms to form a mixture of distorted corner and edge-sharing SeZr3Ni2 square pyramids.
Zr2NiSe4 crystallizes in the monoclinic C2/m space group. Zr(1) is bonded to three equivalent Se(1) and three equivalent Se(2) atoms to form ZrSe6 octahedra that share corners with six equivalent Ni(1)Se6 octahedra, edges with six equivalent Zr(1)Se6 octahedra, and  a faceface with one Ni(1)Se6 octahedra. The corner-sharing octahedral tilt angles are 49°. All Zr(1)-Se(1) bond lengths are 2.71 Å. There is one shorter (2.71 Å) and two longer (2.74 Å) Zr(1)-Se(2) bond lengths. Ni(1) is bonded to two equivalent Se(1) and four equivalent Se(2) atoms to form distorted NiSe6 octahedra that share corners with twelve equivalent Zr(1)Se6 octahedra, edges with two equivalent Ni(1)Se6 octahedra, and faces with two equivalent Zr(1)Se6 octahedra. The corner-sharing octahedral tilt angles are 49°. Both Ni(1)-Se(1) bond lengths are 2.52 Å. All Ni(1)-Se(2) bond lengths are 2.57 Å. There are two inequivalent Se sites. In the first Se site, Se(1) is bonded in a rectangular see-saw-like geometry to three equivalent Zr(1) and one Ni(1) atom. In the second Se site, Se(2) is bonded to three equivalent Zr(1) and two equivalent Ni(1) atoms to form a mixture of distorted corner and edge-sharing SeZr3Ni2 square pyramids.