In this contribution, the evolution of the crystal structure and the consequent effects on the microwave dielectric responses of the Sn 4+ -substituted Li 3 Mg 2−x/3 Sn x Nb 1−2x/3 O 6 (0 ≤ x ≤ 1.5) ceramics were investigated as a function of the doping content. Interestingly, a wide range of solid solution (0 ≤ x ≤ 1.1) was obtained by the complex substitutions of Sn ions, and a composition-driven phase transition from the orthorhombic to cubic phase accompanied by an order−disorder transformation occurring in the range of 0.1 ≤ x ≤ 0.7. During the process of the phase transition, high-resolution transmission electron microscopy images showed the presence of a coherent phase boundary between the orthorhombic and cubic phases, which was formed owing to their similar rock-salt crystal configurations and small mismatches in the subcell−lattice parameters. Besides, the electron diffraction patterns indicated that the specimen with relatively low Sn concentration (x = 0.2) contained reconstructed superlattices. The unique layered structure of the end-member Li 3 Mg 2 NbO 6 constrained the form of the substitution for the dopant ions, where the nonequivalent ions (Sn 4+ ) were expected to enter into the Nb−Mg−Nb clusters in the Nb-rich layers preferentially, which was likely to be the cause of the formation of the reconstructed superlattices. The substitution-induced superlattices were highly related to the low dielectric loss of the specimens, and a small amount of Sn doping (0 ≤ x ≤ 0.3 mol) also lowered the internal strain of the samples. As the Sn concentration increased from 0 to 0.3, the quality factors (Q × f) were significantly enhanced from 91,700 to 118,700 GHz with the emergence of the reconstructed superlattices and the lowered internal strain.