Humic acid (HA) and iron oxide (such as Fe3O4) nanoparticles are widely distributed in soil, and their complex embedded in soil might affect the transport and fate of Cu2+ in the vadose zone, while Cu2+ is a serious threat to the underlying groundwater. In this study, we synthesized a composite of Fe3O4 nanoparticles coated with HA (HA@NPs) using as an amendment a packed sand matrix in the transport column experiments. The impacts of HA content and ion strength (IS) on Cu2+ transport in the unsaturated columns were investigated. The results showed that HA exhibited a stronger inhibition effect on Cu2+ transport, and a higher IS enhanced the mobility of Cu2+ in an unsaturated porous medium in the presence of HA@NPs. The recovery ratio (Rr) of Cu2+ breakthrough in the column decreased from 66.56% to 3.94% while the mass concentration ratio CHA/CNPs increased from 0 to 50 in the HA@NPs complex. The Rr increased by 1.64 times while the IS increased from 0 to 100 mM. Batch adsorption experiments, kinetics and isotherm models, and Fourier transform infrared (FTIR) spectra analysis were implemented to elucidate the underlying mechanism. It was found that HA embedded in the sand matrix could bind Cu2+ by forming stable chelate, while the IS-dependent Cu2+ transport could be attributed to the competitive adsorption between Na+ and Cu2+. Our study demonstrates that the physicochemical environment, as well as the presence of iron oxide nanoparticles and natural organic matter, can significantly impact Cu2+ transport in unsaturated porous medium.