Achieving a high-density, repeatable, and uniform distribution of "hotspots" across the entire surface-enhanced Raman scattering (SERS) substrate is a current challenge in facilitating the efficient preparation of large-area SERS substrates. In this study, we aim to produce homogeneous surface-enhanced Raman scattering (SERS) substrates based on the strong interaction between femtosecond laser pulses and a thin film of colloidal gold nanoparticles (AuNPs). The SERS substrate we obtained consists of irregularly shaped and sharp-edged gold nanoparticle aggregates with specially extruding features; meanwhile, a large number of three-dimensional AuNP stacks are produced. The advantages of such configurations lie in the production of a high density of hotspots, which can significantly improve the SERS performance. When the laser fluence is 5.6 mJ/cm2, the substrate exhibits the best SERS enhancement effect, and a strong SERS signal can still be observed when testing the concentration of R6G at 10-8 mol/L. The enhancement factor of such SERS substrates prepared using femtosecond laser direct writing is increased by 3 orders of magnitude compared to the conventional furnace annealing process. Furthermore, the relative standard deviation for the intensities of the SERS signals was measured to be 5.1% over an area of 50 × 50 μm2, indicating a highly homogeneous SERS performance and excellent potential for practical applications.