Guangxi boasts extensive selenium-rich soils, creating favorable conditions for screening high-quality rice varieties that can be cultivated in this region and determining the optimal selenium fertilizer spraying concentrations for their growth. In this study, three major rice varieties predominantly grown in the area were selected for evaluation (Ge68 Superior 9938, Guiyu 9 and Yexiang Youlisi). A clear water control (CK), Treatment 1 (T1, with the application of 100 g•hm-2 amino acid-based organic selenium), and Treatment 2 (T2, with the application of 200 g•hm-2 amino acid-based organic selenium) were established. Rice yield, brown rice percentage, selenium content in different plant parts, and the levels of certain rice quality indicators were measured. Additionally, the entropy weight-TOPSIS method was employed to evaluate the comprehensive performance of the eight indicators under different treatments. Results indicate that foliar application of selenium (Se) fertilizer significantly increased rice yield by over 8.7% compared to the control group (CK), but had no significant effect on brown rice rate. Under selenium treatment, selenium content in stems, leaves, panicle stems, and grains of all three rice varieties significantly exceeded the control group, with maximum increases of 0.33, 1.12, 0.38, and 0.26 mg/kg, respectively. Regarding nutritional quality, treatment 2 (T2) significantly elevated protein, amylose, lipid, and amino acid content across all three rice varieties. Entropy-weighted TOPSIS analysis indicated that for the rice variety YexiangYouLisi cultivated in Guangxi’s selenium-enriched region, foliar application of selenium fertilizer at a concentration of 200 g•hm-2 was optimal. This concentration not only yielded the highest grain yield and grain quality for this variety but also maintained selenium levels in stems, leaves, panicle stems, and grains within suitable ranges.