We prepare metal films with various thicknesses on liquid substrates by thermal evaporation and investigate the annealing effect on these films. Gold films deposited on a silicone oil surface consist of a large number of branched aggregates, which contains plenty of gold nanoparticles. This characteristic morphology is mainly attributed to the isotropic and free-sustained liquid substrate. Thermal annealing results in the reintegration of nanoparticles; thus, the surface morphology and microstructure of gold films change significantly. The dependence of annealing conditions on the surface-enhanced Raman scattering performance of gold films is studied, in which gold films show favorable Raman activity when annealed at certain annealing temperature and the experimental results are verified by simulation analysis. The study on the optimal annealing temperature of surface-enhanced Raman scattering substrate will pave the way for the potential application of films deposited on liquid surfaces in microfluidics and enhanced Raman detection.