Suspensions with metallic nanoparticles have been widely used to fabricate conductive lines and electrodes for flexible electronic devices under a relatively low processing temperature. This study prepared thiol-stabilized Au nanoparticle suspension and investigated phase transformation of the Au nanoparticle deposits (NPDs) upon heating via in-situ synchrotron radiation X-ray diffraction. With an increasing temperature, the broad diffraction peak of nanosized Au particles with the average diameter of 3nm can be suppressed at around 200°C and soon becomes sharp due to melting and the following solidification. When deposited on the commonly-used electronic substrate, Cu, liquid-solid reaction might occur between the NPDs and the substrate during the thermal process. The low temperature alloying behavior and the formation of the Cu3Au superlattices were manifested by SIMS, XPS and GIXRD.