Surface-enhanced Raman scattering (SERS) has been applied in a range of fields for its high sensitivity and its potential applications in several critical social areas. Reproducible fabricating the SERS substrates in large scale and low cost has been one of the hot topics in SERS researches. In this paper, we assembled the solution processed gold nano clusters with the diameter less than 5 nm into the randomly distributed gold-nanoislands by optimizing the annealing process. We found that the assembling process was slow and could be finely controlled as the annealing temperaturewas within the range of 150~210 ℃. By controlling the assembling process, we can reproducibly fabricate a kind of homogeneous SERS substrate with high density of “hot spots” in large area. These SERS substrates had intense surface enhanced Raman scattering to the monolayer adsorbed on the surface of the gold-nanoislands, and yielded a global enhancement factor as large as 106~107 for the samples annealed at 150~210 ℃. We found that, under the same conditions, the gold nano clusters were firstly fused into tiny gold-nanoislands with the diameter of 10~20 nm as the annealing temperature was within the range of 150~180 ℃. As the annealing temperature was increased to 190~210 ℃, the matrix of tiny gold-nanoislands (10~20 nm) and large gold nanoislands (50~70 nm) could be formed. The spectral characterization has shown that the samples consist of the matrix of tiny and large gold-nanoislands have a higher global enhancement factor than the samples consist of barely tiny gold-nanoislands. At 220 ℃, the gold nanoclusters completely fused into large gold-nanoislands. However, the gaps between the large gold-nanoisland also increased with the fusing process, which induced an exponential decay of the intensity of the electromagnetic field between the gold-nanoislands. As a result, the samples annealed at 220 ℃ has the lowest SERS enhancement factor. In this work, we demonstrated the mechanism of how low-temperature annealing process affects the assembling of the gold nanoclusters. We also showed the relationship between the morphology of the gold-nanoisland and the SERS properties. We provided a facial rout for controllable fabricating the high quality SERS substrates, which has potential applications in the future.