Through monitoring the evolution of the X-ray diffraction peaks, the phase transformation of PVP-protected Ag and Au nanoparticle deposits (NPDs) on electronic substrates of Cu and Ni upon heating in air was investigated via in situ synchrotron radiation X-ray diffraction. With an increasing temperature, the broad diffraction peak of nano-sized Ag and Au particles with the original average diameters of 4.2 nm and 9.6 nm, respectively, became sharp because of particle coarsening and coalescence. Complex phase transitions among Au, Cu, AuCu(3) and CuO(x) were observed, mainly due to the negative enthalpy of mixing between Au and Cu. The interactions between NPDs and the substrates affected the shift of diffraction peaks to lower angles, caused by thermal expansion and also the temperature for the oxide formation. Compared to Au, Ag NPDs did not form intermetallic compounds with Cu and the formation of copper oxides can also be retarded mainly due to the phase separation feature of the Ag-Cu system.