Dyes on ancient silks have been a worth studying field through human's history, although current reports ignore the connection between natural dyes origin and relevant colour reduction methods, which poses an insurmountable obstacle for restoration of historical silks. In this paper, a series of 12 red hue silks from six natural dyes (sappanwood, Chinese madder, safflower, lac, cochineal, dragon's blood) via three different dyeing techniques were used to establish a self‐built precise tandem mass spectrometry (MS/MS) database. With organic solvent extracting on those manual‐dyed silks, ultraperformance liquid chromatography ‐ electrospray ionization ‐ quadrupole time of flight mass spectrometry (UPLC‐ESI‐QTOF‐MS) was utilized to form preliminary MS database for screening and identifying of the potential dyes compounds without standard references. Furthermore, combining the targeted MS/MS mode and the matching threshold of 70.00, a self‐built secondary MS/MS database was successfully established, which contains 33 compounds, 32 chromatograms and 32 MS/MS fragments. As for real sample application, the self‐built precise MS/MS database had revealed that the dyes on two historical silks (Shanghai Museum, China) belong to Chinese madder just with different mordant dyeing ordinal. Additionally, by experimental restoration, visually indistinguishable silks (ΔEab* < 1.5 NBS) were successfully restored. This explorative methodology can further inspire the traceability of biological dyestuffs, which lays instructive foundation on protection and restoration of artefacts, connecting the archaeological science and human art.