Isobutanol synthesis from syngas could be realized on Zn-Cr based catalysts with high activity and selectivity. The ZnO crystal morphology may play an important role on the catalytic performance of Zn-Cr based catalyst for isobutanol synthesis. In this study, a series of Zn-Cr based catalysts with polyhedral or hexagonal ZnO nano-crystal were prepared to explore the effect of morphology and facet of ZnO on direct synthesis of isobutanol from syngas. We find that the interaction between ZnO and ZnCr2O4 phases poses a crucial factor for the catalytic performance. Compared with sole ZnO or Zn-Cr catalyst, Zn-Cr/p-ZnO and Zn-Cr/h-ZnO catalysts with a binary crystal structure of ZnO and ZnCr2O4 show higher total alcohol and isobutanol selectivity. Furthermore, the hexagonal ZnO of Zn-Cr/h-ZnO catalyst exposes more (0 0 0 1) facets compared to the polyhedral ZnO of Zn-Cr/p-ZnO catalyst, resulting in stronger interaction between ZnO and ZnCr2O4 phases for Zn-Cr/h-ZnO catalyst. The most excellent catalytic performance could be obtained on Zn-Cr/h-ZnO catalyst with the highest CO conversion (22.1%) as well as isobutanol selectivity (24.4 wt%). Thus, exposing more (0 0 0 1) facets of h-ZnO could significantly improve the catalytic performance for isobutanol synthesis from syngas, which provides a new perspective of the face-activity relationship on Zn-Cr based catalyst.