3D porous iron (Fe) scaffolds with interconnected open pores are promising candidates for bone repair. However, the bare 3D porous Fe scaffolds lack of antibacterial activity and the ability for cell adhesion. Herein, atomic layer deposition technique was used to deposit nanometer-thick zinc oxide (ZnO) layer onto the skeleton of 3D porous Fe scaffolds with interconnected open pores. The effect of ZnO thin film on the in vitro degradation behavior, antibacterial activity and cytocompatibility of 3D porous Fe scaffolds was systematically evaluated. The results showed that a dense ZnO thin film with a thickness of 76 nm was uniformly deposited on the skeleton of the porous Fe scaffolds. The thickness of ZnO thin film could be easily controlled by the deposition cycles. The deposited ZnO thin film significantly reduced the degradation rate of porous Fe scaffolds and the fabricated ZnO coated porous Fe scaffolds demonstrated strong antibacterial ability against both Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus, while did not significantly affect cytocompatibility and could also promote cell adhesion.