The co-application of N and Fe can improve wine grape composition and promote the formation of flavor compounds. To understand the effects of foliar co-application of N and Fe on wine grape quality and flavonoid content, urea and EDTA-FE were sprayed at three different developmental stages. Urea and EDTA-Fe were sprayed during the early stage of the expansion period, at the end of the early stage of the expansion period to the late stage of the veraison period, and during the late stage of the veraison period. The results demonstrated that the co-application of urea and EDTA-Fe, particularly N application during the late stage of the veraison period and Fe application during the early stage of the berry expansion period (N3Fe1), significantly improved grape quality. Specifically, the soluble solid content of berries increased by 2.78–19.13%, titratable acidity decreased by 6.67–18.84%, the sugar-acid ratio became more balanced, and yield increased by 13.08–40.71%. Further, there was a significant increase in the relative content of amino acids and flavonoids. In conclusion, the application of Fe and N fertilizers at the pre-expansion and late veraison stages of grapes can significantly improve the quality and yield of berries; ultimately, this establishes a foundation for future improvement in the nutritional value of grapes and wine.