A family of two-dimensional (2D) Zn-based metal-organic frameworks (MOFs) with exitonic emission have been successfully synthesized under hydrothermal conditions. When isophthalic acid ligands with different substitutions are introduced, the crystal structures and fluorescence properties are significantly changed. Hirshfeld surface calculation is used to study the nuances of diverse substitutions during the construction of all of the crystals. The solid fluorescence results indicate that there are obvious two-channel emissions, including intralayer excimers and interlayer trapped excitons, both in 1 and 2 with a double-layer structure and in 3 with a single-layer structure, mainly exhibiting intralayer emission. Furthermore, the fluorescence changes on morphology transformations are explored after mechanical exfoliation consisting of grinding and ultrasonicaation of MOFs 1-3. The regulation and control of crystal structure and morphology can suppress emission based on interlayer excitons, achieving adjustment of the overall emitting color. To the best of our knowledge, this is the first report of 2D bilayer MOFs with dual-channel emissions, which provides a new structural model for synthesizing new exciton materials.