The effect of current density on the morphology of Zn electrodeposits prepared by a flow-channel cell was investigated by scanning electron microscopy (SEM). It was found that the morphology of Zn electrodeposits evolves from thin-layered hexagonal η-phase crystals to pyramidal η-phase particles with increasing the current density. The morphological evolution at various flow rates was also examined and the results show that the morphological evolution at a lower flow rate is more remarkable than that at a higher flow rate with increasing the current density. To reveal the mechanism of the morphological evolution in detail, the atomic configuration on both (0001)η and { 1100 }η planes under different current densities was investigated, it was noted that a specify current density could provide a good condition for the layered epitaxial growth of hexagonal η-phase.