High-quality grape raw materials are fundamental for producing premium wine. Ensuring the quality of grape raw materials, particularly enhancing their phenolic profiles, significantly improves wine flavor. Therefore, this study focused on ‘Cabernet Franc’ grapes, where a 0.1% chitooligosaccharide (COS) solution was foliar sprayed during the green pea stage, the onset of veraison stage, and the mid-ripening stage to investigate the impact of exogenous COS treatment on the accumulation of phenolic compounds in grape berries. The results revealed that COS treatment during the green pea and the onset of veraison stages significantly increased the levels of total phenolic, total flavonoid, and total anthocyanin in grapes, with distinct effects on flavanols, phenolic acids, flavonols, and stilbenes, respectively. Eight key compounds most significantly influenced by the treatment were identified through orthogonal partial least squares discriminant analysis (OPLS-DA) and machine learning screening. Specifically, treatment during the green pea stage had a significant impact on total soluble solids, proanthocyanidin B1, catechin, and vanillic acid, while veraison treatment notably affected petunidin-3-O-(6″-O-p-coumaryl)-glucoside, cyanidin-3-O-(6″-O-p-coumaryl)-glucoside, cyanidin-3-O-glucoside and isorhamnetin. This study could provide valuable data references and theoretical support for applying COS in wine grapes and regulating high-quality raw materials.