The interface effect is one of the most important factors that strongly affect the structural transformations and the properties of nano-/submicro-crystals under pressure. However, characterization of the granular boundary changes in materials is always challenging. Here, using tetrakaidecahedral Zn2SnO4 microcrystals as an example, we employed alternating current impedance, X-ray diffraction methods and transmission electron microscopy to elucidate the effect of the interface on the structure and electrical transport behavior of the Zn2SnO4 material under pressure. We clearly show that grain refinement of the initial microcrystals into nanocrystals (approximately 5 nm) occurs at above 12.5 GPa and is characterized by an anomalous resistance variation without a structural phase transition. A new phase transition pathway from the cubic to hexagonal structure occurs at approximately 29.8 GPa in Zn2SnO4. The unexpected grain refinement may explain the new structural transition in Zn2SnO4, which is different from the previous theoretical prediction. Our results provide new insights into the link between the structural transition, interface changes and electrical transport properties of Zn2SnO4.