Abstract: One primary goal of self-assembly in nanoscale regime is to implement multifunctional binary nanoparticle superlattices into practical use. In the last decade, considerable effort has been put into the fabrication of binary nanoparticle superlattices with controllable structure and stoichiometry. However, limited effort has been made in order to improve the stability of these binary nanoparticle superlattices, which is a prerequisite for their potential application. In this work, we demonstrate that the carbon deposition from specimen contamination can play an auxiliary role during the heat treatment of binary nanoparticle superlattices. With the in-situ carbon matrix formation, the thermal stability of CoAu 13 binary nanoparticle superlattices is unambiguously enhanced.