Free amino acid (FAA) profile is an important indicator of the quality of fruit and fruit product. Foliar nutrient diagnosis has been used for crop yield prediction for decades but not for fruit quality evaluation. Concentrations of 11 leaf nutrients including N, P, K, Ca, Mg, S, Fe, Mn, Cu, Zn, and B at stages of terminal shoot maturation and fruit development and fruit FAA profile at harvest were examined in longan in South China. The relation between leaf nutrient and fruit FAA was then investigated by multiple stepwise regression analysis. Foliar N content was greatest among the nutrients among the detected elements at both stages. Twenty-nine FAAs were determined in longan flesh, with alanine (19.9%), γ-aminobutyric acid (17.5%), glutamic acid (15.2%), and asparagine (10.7%) as the main components. Flesh individual FAA, essential amino acid (AA), umami-, and sweet and bitter taste AA strongly depended on foliar nutrients. However, the relation between flesh FAAs and foliar nutrients varied with FAA species. Leaf N was the dominant indicator for most pulp FAAs at two growth stages, while other nutrients (e.g., B, Zn, P, K, Ca, Mg) also played versatile roles on flesh FAAs. This work provides a novel tool to predict fruit FAAs via foliar nutrient diagnosis, which supports the practicality of producing specific target fruit or improving fruit quality through regulation of fertilization strategies in fruit production.