Identification of the active site is important in developing rational design strategies for solid catalysts but is seriously blocked by their structural complexity. Here, we use uniform Cu nanocrystals synthesized by a morphology-preserved reduction of corresponding uniform Cu2O nanocrystals in order to identify the most active Cu facet for low-temperature water gas shift (WGS) reaction. Cu cubes enclosed with {100} facets are very active in catalyzing the WGS reaction up to 548 K while Cu octahedra enclosed with {111} facets are inactive. The Cu-Cu suboxide (CuxO, x ≥ 10) interface of Cu(100) surface is the active site on which all elementary surface reactions within the catalytic cycle proceed smoothly. However, the formate intermediate was found stable at the Cu-CuxO interface of Cu(111) surface with consequent accumulation and poisoning of the surface at low temperatures. Thereafter, Cu cubes-supported ZnO catalysts are successfully developed with extremely high activity in low-temperature WGS reaction.Nanocrystals display a variety of facets with different catalytic activity. Here the authors identify the most active facet of copper nanocrystals relevant to the low-temperature water gas shift reaction and further design zinc oxide-copper nanocubes with exceptionally high catalytic activity.