Amino acids are a type of organic nutrient essential for plant growth and can be used as fertilizer in agriculture. However, the effects of foliar application of amino acids on fragrant rice performances have rarely been reported. In the present study, glutamate and phenylalanine were foliar applied to fragrant rice plants at the initial heading stage in a two-year field experiment. The grain yield, yield-related traits, grain quality parameters, volatiles, and chlorophyll were determined. An untargeted metabolomics analysis using LC-MS was used to further explore the regulation mechanism. The results showed that foliar application of glutamate and phenylalanine significantly increased the seed-setting rate, grain yield, and the contents of chlorophyll a, chlorophyll b, and carotenoid. GC-MS analysis showed that volatiles including 2-acetyl-1-pyrroline, heptanal, 2-pentylfuran, and D-limonene, were significantly affected by glutamate and/or phenylalanine. Higher grain 2-acetyl-1-pyrroline content was observed in phenylalanine treatment in both years. Glutamate treatment significantly increased globulin, prolamin, and glutelin contents. Untargeted metabolomics analysis showed that glutamate regulated 104 metabolites in leaves and 93 metabolites in grains, and phenylalanine regulated 132 metabolites in leaves and 123 metabolites in grains.