Corn stalk core (CSC) is low-cost and sustainable biomaterials, which can be used as a filtration material due to its naturally porous structure. A simple method of chemical precipitation was applied to load ZnO nanoparticles (ZnO NPs) into the core, which was used for water purification and sterilization. The different zinc sources had an obvious effect on various morphology and chemical characteristics of ZnO immobilized in CSC, leading to a variety of antibacterial activities. The composite biofilter prepared from zinc acetate showed the excellent antibacterial effect, and the antibacterial rates of Escherichia coli and Staphylococcus aureus reached 94.5% and 90.5% respectively, after filtration for 5 min. The antibacterial mechanism of the hybrid column might be ascribed to the interception of bacteria by hierarchical porous structure of CSC, resulting in an increase of the physical friction with nanoparticles and chemical reactions with reactive oxygen species (ROS) and hydrated zinc ions. Consequently, the cell membranes of bacteria were damaged and the components in cells were leaked, finally leading to the death of bacteria.