The application of Ag nanostructures to surface-enhanced Raman scattering (SERS) is hindered by their chemical instability. Fabrication of durable Ag-based SERS substrates is therefore of great significance in practical applications. In this work, ultrathin C-layer-encapsulated Ag nanoparticle arrays (UCL-Ag-NAs) are successfully fabricated on the surface of indium-tin-oxide (ITO) glass, using a hydrothermal method, for use as durable SERS substrates. The problem of Ag nanoparticles dissolving during the hydrothermal process is solved by using ZnO powder as a pH-buffering reagent. The SERS signal intensity of UCL-Ag-NAs decreases, accompanied by an improvement in Raman signal stability, as the C-layer thickness increases. Raman spectra show that the SERS signal intensities obtained from UCL-Ag-NAs with C-layers of 4.5 nm and 7.3 nm stored for 180 days are 64.9% and 77.8% of those obtained from as-prepared counterparts. The SERS intensity of the UCL-Ag-NA (C-layer of 4.5 nm) is 152.7% that of the bare Ag NA after 180 days of storage. XPS spectra confirm that the C-layer effectively suppresses the oxidation of the Ag NA. This methodology can be generalized to improve the durability of other dimensional Ag nanostructures for SERS applications.