The topsoil temperature in arid areas of Xinjiang, China can be up to about 80°C in summer. This may significantly affect the chemical properties of soil humic substances. However, the effects of high temperature on characteristics of soil humic substances and their complexation with toxic metals are still poorly known. In the present study, binding of Hg(II) to unheated soil humic substances and heated soil humic substances from sandy soils was comparatively investigated using three-dimensional excitation–emission matrix (EEM) fluorescence spectroscopy. Two fluorescent peaks (peak I at Ex/Em = 365–370/470–474 nm; peak II at Ex/Em = 270–275/468–472 nm) identified as humic-like fluorescence were observed in the EEM spectra of humic substances. Both peaks were clearly quenched by Hg(II), indicating the strong interaction of humic-like substances with Hg(II), and showed blue shifts after heat treatment. Heat treatment caused an increase of the fraction of accessible fluorophore (f _a), binding sites number (n) and effective quenching constants (logK _a), indicating that more binding sites in humic substances could bind Hg(II) and form more stable humic substances–Hg(II) complexes after heat treatment. However, a decrease of binding constants (logK _b) suggested that heat treatment would reduce the binding capacity of each binding site of humic substances to Hg(II). This study implies the transport of Hg(II) may be affected by high temperature in the arid zone due to the modification of the physicochemical properties of humic substances in soil.