Synchrotron (SR) X-ray radiation induced gold nanoparticles (AuNPs) creation. AuNPs are aggregated into clusters with the increase of the X-ray irradiation time. The aggregation characteristics are explained by considering how to modify the nanoparticles deposition process by Derjaguin-Landau-Verwey-Overbeek (DLVO) theory interactions and van der Waals forces. We demonstrated surface enhanced Raman scattering (SERS) measurement for 4,4'-Bipyridine (4bpy) as the Raman active molecule using the AuNPs produced by SR on a Si substrate. This structure brought the success of detection of 1 nM 4bpy. This method allows easy fabrication of SERS-active area in a microfluidic device.