By combining the excellent surface-enhanced Raman scattering (SERS) activity of Ag nanoparticles (AgNPs), the well-separated pyramid arrays of the pyramidal silicon (PSi) and unique physical/chemical properties of molybdenum disulfide (MoS₂), the MoS₂@AgNPs@PSi substrate shows high performance in terms of sensitivity, uniformity, reproducibility and stability. By using rhodamine 6G (R6G) as probe molecule, the SERS results indicate that the MoS₂@AgNPs@PSi substrate is superior to the AgNPs@PSi, AgA@PSi (the second annealing of the AgNPs@PSi) and the MoS₂@AgNPs@flat-Si substrate. The MoS₂@AgNPs@PSi substrate also shows the reasonable linear response between the Raman intensity and R6G concentration. The maximum deviations of SERS intensities from 20 positions on a same MoS₂@AgNPs@PSi substrate and 10 MoS₂@AgNPs@PSi substrates in different batches are less than 7.6% and 9%, respectively, revealing the excellent uniformity and reproducibility of the substrate. Besides, the SERS substrate has a good stability, the Raman intensity of the MoS₂@AgNPs@PSi substrate only drop by 15% in a month. The corresponding experimental and theoretical results suggest that our proposed MoS₂@AgNPs@PSi substrate is expected to offer a new and practical way to accelerate the development of label-free SERS detection.