The excessive use of chemical fertilizers in the Guanxi honey pomelo production area has led to severe soil acidification and magnesium (Mg) deficiency, adversely affecting pomelo fruit quality. To address this issue, an integrated nutrient optimization model crucial for ensuring the sustainable and environmentally friendly development of the Guanxi honey pomelo industry has been explored. In a three-year experiment, two fertilizer treatments were implemented: a farmer fertilizer practice (FP) and an NPK reduction plus foliar Mg fertilizer (OPT + fMg). We investigated the impact of this integrated optimized fertilization measure on pomelo fruit quality from three aspects: flavor (sugars and organic acids), nutrition (vitamin C and mineral elements), and antioxidant properties (phenolics, flavonoids, and phytic acid). The results revealed that the OPT + fMg treatment improved fruit flavor by reducing acidity (titratable acid, citric acid, and quinine), while having a minimal impact on sugar components (sucrose, fructose, and glucose). Additionally, the OPT + fMg treatment increased the total phenolics, total flavonoids, and phytic acid in the fruit peel, enhancing its potential antioxidant quality. However, the OPT + fMg treatment reduced the mineral nutrient quality (excluding calcium) in the fruit. As for the fruit developmental period, the OPT + fMg treatment significantly increased the total flavonoid concentration in the peel from the mid-expansion fruit stage, followed by notable increases in phytic acid in the peel during the mid-to-late expansion fruit stage. The total phenolic concentration in the peel significantly rose only during the late fruit development stage. The most pronounced effect was observed on phytic acid in both peel and pulp. The influence of the OPT + fMg treatment on the mineral nutrients (excluding calcium) primarily occurred during the mid-to-late expansion fruit stage. Overall, the OPT + fMg treatment significantly improved the comprehensive nutritional quality of pomelo fruit, providing valuable insights for scientifically reducing fertilizer application while enhancing fruit quality.