To investigate the impact of storage duration on the quality of Yunnan black tea, this study selected seven samples of the same grade produced by the same manufacturer stored under the same conditions in the period between 2011 and 2024. Their flavor qualities were characterized by sensory evaluation, routine physicochemical analysis, high performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) combined with multivariate statistical analysis. Results indicated that with increasing storage duration, the aroma characteristics shifted from floral, fruity and sweet notes towards a woody note, and the smooth, sweet, and mellow taste diministed, accompanied by the emergence of a sour taste. Among non-volatile components, the contents of tea polyphenols, theaflavins, and free amino acids exhibited a decreasing trend with prolonged storage, while those of thearubigins, gallic acid, and caffeine increased. Theaflavin content peaked (6.32%) after three years of storage before declining. A total of 64 volatile compounds were identified, predominantly ketones (21.88%), aldehydes (21.88%), alcohols (15.62%), and hydrocarbons (15.62%). Among these, the contents of nine key flavor markers (variable important in the projection (VIP) > 1 and odor activity value (OAV) ≥ 1), including β-cyclocitral and linalool, decreased with extended storage duration, while those of dihydroactinidiolide, phenylacetone, and dehydro-β-ionone increased. Principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) indicated storage duration as the core driving factor for quality variation in Yunnan black tea, with an optimal storage period of 1–3 years. This study provides insights into changes in the flavor quality of Yunnan black tea over varying storage periods and the underlying mechanism of its characteristic aroma formation.