Long-term aging has traditionally been associated with issues such as color fading and oxidation; therefore, it limits grape wine production. Here, we analyzed 90 bottles of mulberry wine aged for various periods (up to 12 years) and observed unique trends in color, flavor, and aroma compounds during prolonged aging. Results from Somers and methylcellulose precipitation (MCP) assays indicated that the tannin and anthocyanin concentrations in newly fermented mulberry wines were 167 to 216 mg/L and 1.04 to 1.37 g/L, respectively. The total phenolics, tannins, and anthocyanin contents exhibited significant negative correlations with aging years, while the non-bleachable pigment content and hue showed positive correlations with aging times. High-performance liquid chromatography–electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) analysis further revealed a positive correlation between the content of pyranoanthocyanins (including cyanidin-3-O-glucoside-pyruvic acid, cyanidin-3-O-glucoside-acetaldehyde, cyanidin-3-O-glucoside-4-vinocatechol, and cyanidin-3-O-glucoside-4-vinophenol) and aging times, whereas the impacts of aging on the polymeric pigment (cyanidin-3-O-glucoside-epicatechin) were not observed. This suggests that the anthocyanins in mulberry wine primarily transformed into pyranoanthocyanins rather than polymeric pigments during aging. The aging-induced reductions in protein, polysaccharide, and key aroma compounds (contributing to the fruity, sweet and floral odors) remained unaffected by prolonged aging.