ABSTRACT In this work, dyed samples were self-prepared from two methods including madder dyeing and mordant dyeing by madder combined with Al3+ at different temperatures, and their kinetics and isothermal adsorption were both discussed. Weber–Morris diffusion model and Freundlich model were found to be more suitable in dyeing for kinetics and thermodynamics. Through SEM, FTIR and fastness tests, the dyeing performances were displayed and the possible structure between madder dyes and the complex with Al3+ were illustrated. By molecular docking, madder dyes showed combination with glutamic acid predominantly. After introducing metal ion, the shortage of hydrogen bonds length was observed. It was initially employed to elucidate the potential binding modes between dyes and proteinaceous fibers. Overall, through experimental dyeing and curve fitting, this study provided insights into the dyeing mechanism of madder-associated dyestuffs on silk. Moreover, molecular docking elucidated the dyeing mechanism further, highlighting that the presence of metal ion enhances the firmness of the staining. The elucidation of dyeing mechanism not only provided valuable theoretical support for color restoration but also shed light on the practically modify of methods in obtaining ideal color. These results could serve as inspiration for conservators to maintain the vibrancy and longevity of dyed silks.