The physical and chemical reactions between heavy metals in landfill leachate and soil may change the microstructure of soil, then the diffusion and migration of heavy metals and other toxic substances, threaten human health and surrounding environment. In order to investigate the effects of heavy metal contamination on macroscopic water retention and microstructure of loess, the soil-water characteristic curves of Pb-contaminated loess were measured by axial translation technique. Characterization of mesoscopic structure changes was clarified by scanning electron microscopy (SEM), mercury injection (MIP), X-ray diffraction (XRD) and Zeta potential. The results show that the air-entry values of Pb-contaminated loess decrease with the increase of Pb-concentration. When the lead pollution concentration increases from 0 mg/kg to 2 000 mg/kg, the air-entry values decrease from 19.18 kPa to 12.12 kPa, indicating that lead contamination lead to a decrease in water retention. On the contrary, the permeability increases with the increase of lead concentrations. The saturated permeability coefficient increases from 7.92×10–8 m/s to 3.73×10–7 m/s. The physicochemical reaction and reduction of Zeta potential caused by lead contamination produce flocculation structure, and the proportion of small pores decreases while that of medium pores increases. The microscale structural evolution has a good correspondence, induced by the lead contamination, with macroscopic water retention capacity and permeability. The results can provide important parameters for the study of unsaturated seepage and solute transport in heavy metal contaminated sites.