Silk artifacts are commonly dyed with natural dyes, the composition of which reflects their historical context. In this study, silver nanoparticles (AgNPs) were modified with KI solution at room temperature to produce KI-functionalized Surface-enhanced Raman spectroscopy (SERS) substrates. The optimized substrate, prepared at a 3:1 ratio AgNPs-to-KI ratio solution, exhibited superior localized surface plasmon resonance (LSPR) properties, which significantly increased Raman signals of dye molecules while effectively reducing background interference from the substrate. The relative standard deviations (RSD) of alizarin as a molecular probe was 3.47 %, with an enhancement factor (EF) of approximately 6.16 × 106. SERS reference fingerprint spectra were established for five representative anthraquinone natural dyes: dyer's madder (Rubia tinctorum), Indian madder (Rubia cordifolia), Japanese madder (Rubia argyi), lac insect (Kerria lacca) and cochineal (Dactylopius coccus). The method was then applied to analyze dyes in silk artifacts from the collection of the Hungarian Museum of Applied Arts, where alizarin, purpurin, and laccaic acid were detected in a single silk fiber. The proposed KI-AgNPs SERS technique provides a minimally invasive, rapid, reliable and highly specific tool for identifying trace natural dyes in silk artifacts.