MgY2Se4 is Spinel-like structured and crystallizes in the orthorhombic Pnma space group. Mg(1) is bonded to one Se(2), one Se(3), and two equivalent Se(1) atoms to form MgSe4 tetrahedra that share corners with two equivalent Y(1)Se6 octahedra, corners with four equivalent Y(2)Se6 octahedra,  an edgeedge with one Y(2)Se6 octahedra, and edges with two equivalent Y(1)Se6 octahedra. The corner-sharing octahedral tilt angles range from 59-66°. There are two inequivalent Y sites. In the first Y site, Y(1) is bonded to two equivalent Se(1), two equivalent Se(2), and two equivalent Se(3) atoms to form YSe6 octahedra that share corners with four equivalent Y(2)Se6 octahedra, corners with two equivalent Mg(1)Se4 tetrahedra, edges with two equivalent Y(1)Se6 octahedra, edges with two equivalent Y(2)Se6 octahedra, and edges with two equivalent Mg(1)Se4 tetrahedra. The corner-sharing octahedral tilt angles range from 50-53°. In the second Y site, Y(2) is bonded to one Se(2), one Se(3), and four equivalent Se(1) atoms to form YSe6 octahedra that share corners with four equivalent Y(1)Se6 octahedra, corners with four equivalent Y(2)Se6 octahedra, corners with four equivalent Mg(1)Se4 tetrahedra, edges with two equivalent Y(1)Se6 octahedra, and  an edgeedge with one Mg(1)Se4 tetrahedra. The corner-sharing octahedral tilt angles range from 46-53°. There are three inequivalent Se sites. In the first Se site, Se(1) is bonded in a rectangular see-saw-like geometry to one Mg(1), one Y(1), and two equivalent Y(2) atoms. In the second Se site, Se(2) is bonded in a rectangular see-saw-like geometry to one Mg(1), one Y(2), and two equivalent Y(1) atoms. In the third Se site, Se(3) is bonded to one Mg(1), one Y(2), and two equivalent Y(1) atoms to form distorted corner-sharing SeY3Mg trigonal pyramids.
MgY2Se4 is Spinel-like structured and crystallizes in the orthorhombic Pnma space group. Mg(1) is bonded to one Se(2), one Se(3), and two equivalent Se(1) atoms to form MgSe4 tetrahedra that share corners with two equivalent Y(1)Se6 octahedra, corners with four equivalent Y(2)Se6 octahedra,  an edgeedge with one Y(2)Se6 octahedra, and edges with two equivalent Y(1)Se6 octahedra. The corner-sharing octahedral tilt angles range from 59-66°. The Mg(1)-Se(2) bond length is 2.61 Å. The Mg(1)-Se(3) bond length is 2.53 Å. Both Mg(1)-Se(1) bond lengths are 2.60 Å. There are two inequivalent Y sites. In the first Y site, Y(1) is bonded to two equivalent Se(1), two equivalent Se(2), and two equivalent Se(3) atoms to form YSe6 octahedra that share corners with four equivalent Y(2)Se6 octahedra, corners with two equivalent Mg(1)Se4 tetrahedra, edges with two equivalent Y(1)Se6 octahedra, edges with two equivalent Y(2)Se6 octahedra, and edges with two equivalent Mg(1)Se4 tetrahedra. The corner-sharing octahedral tilt angles range from 50-53°. Both Y(1)-Se(1) bond lengths are 2.91 Å. Both Y(1)-Se(2) bond lengths are 2.88 Å. Both Y(1)-Se(3) bond lengths are 2.84 Å. In the second Y site, Y(2) is bonded to one Se(2), one Se(3), and four equivalent Se(1) atoms to form YSe6 octahedra that share corners with four equivalent Y(1)Se6 octahedra, corners with four equivalent Y(2)Se6 octahedra, corners with four equivalent Mg(1)Se4 tetrahedra, edges with two equivalent Y(1)Se6 octahedra, and  an edgeedge with one Mg(1)Se4 tetrahedra. The corner-sharing octahedral tilt angles range from 46-53°. The Y(2)-Se(2) bond length is 2.85 Å. The Y(2)-Se(3) bond length is 2.86 Å. There are two shorter (2.92 Å) and two longer (2.93 Å) Y(2)-Se(1) bond lengths. There are three inequivalent Se sites. In the first Se site, Se(1) is bonded in a rectangular see-saw-like geometry to one Mg(1), one Y(1), and two equivalent Y(2) atoms. In the second Se site, Se(2) is bonded in a rectangular see-saw-like geometry to one Mg(1), one Y(2), and two equivalent Y(1) atoms. In the third Se site, Se(3) is bonded to one Mg(1), one Y(2), and two equivalent Y(1) atoms to form distorted corner-sharing SeY3Mg trigonal pyramids.