It is very vital to construct the dense hot spots for the strong surface-enhanced Raman scattering (SERS) signals. We take full advantage of the MoS2 edge-active sites induced from annealing the Ag film on the surface of the MoS2. Furthermore, the composite structure of Au-Ag bi-metal nanoparticles (NPs)/MoS2 hybrid with pyramid structure is obtained by the in situ grown AuNPs around AgNPs, which serves the optimal SERS performance (enhancement factor is ~9.67 × 109) in experiment. Due to the introduction of AuNPs with the simple method, the denser hot spots contribute greatly to the stronger local electric field, which is also confirmed by the finite-different time-domain (FDTD) simulation. Therefore, the ultralow limit of detection (the LOD of 10-13 and 10-12 M respectively for the resonant R6G and non-resonant CV), quantitative detection and excellent reproducibility are achieved by the proposed SERS substrate. For practical application, the melamine molecule is detected with the LOD of 10-10 M using the proposed SERS substrate that has the potential to be a food security sensor.