Here we report the electronic and local atomic structure of thiol-stabilized Au∼98Ag∼46(SR)60 nanoclusters investigated by synchrotron radiation-based X-ray absorption fine structure (XAFS). Au L3-edge X-ray absorption near edge fine structure (XANES) was used to examine the d band character of Au, which is highly related to the electronic, magnetic and catalytic activities of Au. It was observed that the d band hole population of Au in Au∼98Ag∼46(SR)60 was higher than that of bulk Au. The formation of the AuAg alloy was confirmed by extended X-ray absorption fine structure (EXAFS). The EXAFS results also suggested that Au atoms in Au∼98Ag∼46(SR)60 nanoclusters preferred to occupy the metal core sites, while the Ag atoms were mainly on the surface.