To address the limited flavor complexity of wolfberry (Lycium barbarum L.) puree and prominent acidity of Prunus humilis Bunge puree, multi-quality synergistic optimization of the compound beverage was performed, with apple juice concentrate as the sugar–acid modifier. Single-factor experiments and Box-Behnken response surface methodology were employed, with an AHP–CRITIC weighted evaluation system integrating sensory score, chroma (C*ab) and total soluble solids. The optimal formulation (wolfberry/P. humilis mass ratio 2.8:1, 65.0% compound puree, 3.0% apple juice concentrate) achieved a relative error of 1.82% between experimental and predicted comprehensive scores. The optimized beverage had 13.2 °Brix soluble solids, a sugar–acid ratio of 34.7, and total phenolic, flavonoid, and polysaccharide contents of 116.75, 7.78, and 420.30 mg/100 g, respectively. GC-IMS revealed the flavor fingerprint characteristics of raw materials and final product, with four characteristic components (terpenes from P. humilis; aldehydes/esters from? wolfberry) retained in the product; electronic tongue showed a balanced taste profile with weak bitterness and astringency. This study offers a methodological reference for multi-quality synergistic optimization and flavor fingerprint evaluation of specialty berry beverages.