Whey utilization remains low, and the deep processing of Mongolian parched rice is insufficient; therefore, their co-fermentation has considerable potential for high-value utilization. In this study, whey and parched rice were used as substrates to prepare a fermented beverage by co-fermentation with lactic acid bacteria and Saccharomyces cerevisiae, with the aim of elucidating the changes in quality and flavor before and after fermentation. Process parameters were optimized by single-factor experiments, Plackett–Burman design, and Box–Behnken response surface methodology. Changes in volatile compounds and non-volatile metabolites before and after fermentation were analyzed by HS-SPME-GC-MS and UPLC-MS, respectively. The results showed that the optimum conditions were a lactic acid bacteria inoculum of 0.60 wt.%, a fermentation time of 32 h, and a fermentation temperature of 37 °C. Under these conditions, the sensory score and titratable acidity reached 93.68 and 70.94 °T, respectively. Compared with the unfermented sample, the DPPH and ABTS radical-scavenging activities increased by 54.22% and 44.90%, respectively, after fermentation, while the total phenolic content increased by 322.23 mg GAL·L-1. A total of 257 volatile compounds were identified. After fermentation, the relative contents of esters and alcohols increased, whereas pyrazines and some carbonyl compounds decreased. The key aroma profile shifted from raw material-derived notes represented by compounds such as 2,6-diethylpyrazine to a fruity and floral aroma system dominated by ethyl hexanoate, ethyl isovalerate, and 2-phenylethanol. Metabolic pathway analysis indicated that phenylalanine metabolism, nicotinate and nicotinamide metabolism, and amino acid biosynthesis were closely associated with flavor formation and quality improvement. Co-fermentation significantly enhanced the antioxidant activity of the beverage and reshaped its flavor profile, providing a theoretical basis for the high-value utilization of whey and the development of regionally distinctive cereal resources.