This study investigated the structural characteristics and chemical compositions of melanoidins in Monascus vinegar at different brewing stages through spectroscopic and HPLC-MS analysis. The results showed that melanoidins were exogenously added through the miwu rinsing process and not formed during fermentation. During aging, proteins and phenols continuously participated in melanoidin formation, increasing particle size, molecular weight, and antioxidant ability. FT-IR and 1H NMR spectra revealed that melanoidins mainly comprised carbohydrates, proteins, and phenols. The identified components included 10 carbohydrates (glucose being the main one), 18 amino acids, 8 free phenolics, and 15 bound phenolics (with ferulic acid as the major phenolic compound). Phenolic compounds, mainly bound through ester bonds, played a key role in improving the antioxidant activity of melanoidins. These findings provide a theoretical basis for regulating melanoidin formation during Monascus vinegar production.