Selenium (Se) supplementation through plant-based foods is easy to implement and effective; therefore, it is important to explore the Se-enrichment ability of staple grains and analyze their quality. The purpose of this study was to investigate the effects of foliar application of Se on the quality, Se-enriched capacity, organic Se composition and content of rice under field cultivation. The results showed that exogenous Se application at 80 mg L−1 contributed the most to the yield, and eight elements differed accordingly to the application of Se, promoted the accumulation of Se-containing organic matter in rice grain. This indicates that rational foliar application of Se can effectively improve the quality of rice grains. Moreover, selenomethionine (SeMet), selenocysteine (SeCys2), and Se-methylselenocysteine (Se-MeSeCys) are important components of Se-enriched in hydrolyzed proteins in grains. Based on these results, foliar spraying of Se is a suitable method to supplement rice with additional Se and can improve the yield and quality of rice grains, particularly the quality of organic Se and Se-containing amino acids.