Surface-enhanced Raman spectroscopy (SERS) is considered as a powerful analytical tool with a fingerprint-level resolution. Nevertheless, it is still challenging to fabricate large-area, sensitive, and reproducible SERS substrates through facile and cost-effective process. Herein, a novel double-layer rotational symmetry cantilever (DRSC)-based probe lithography was proposed for the facile and cost-effective fabrication of wafer-scale ordered micro/nanostructures towards SERS applications. Using finite element simulation, the architecture of DRSC was optimized, and its strength and fatigue were checked. Several typical fabrication parameters were evaluated using the DRSC-based probe lithography. The results indicated that the proposed lithography exhibited identical stiffness in all horizontal directions, and can effectively suppress the horizontal drift and achieve high-precision fabrication under the condition of high-speed reciprocating processes. Several high-quality micro/nanostructures were achieved to demonstrate its excellent ability in large-area and high-precision fabrication. SERS spectra of malachite green (MG) indicated an impressive enhancement, excellent stability, and high reproducibility (including intra-substrate and batch-to-batch sampling), and practical applications of prepared SERS substrates were demonstrated by detecting MG residues from various water environments and fish scales. This study provides a promising approach for the facile and cost-effective fabrication of large-area, sensitive, and reproducible SERS substrates.