With the growing global demand for rice and the urgent need to enhance sustainable production, ratoon rice systems and selenium (Se) biofortification technologies have become important strategies. This study investigated the effects of the foliar application of ethylenediaminetetraacetic acid Se (EDTA-Se) during key growth stages of the main rice season on the yield, grain quality, and Se accumulation in ratoon rice. Two rice varieties—Fengliangyouxiang-1 (FLYX1) and Jinliangyouhuazhan (JLYHZ)—were selected for a two-year field experiment. A systematic analysis was performed on yield components, processing quality, appearance quality, nutritional quality, and Se speciation. The results showed that under an equivalent total amount of spraying EDTA-Se, the best effect on improving the yield, grain quality, and grain Se content of ratoon rice was observed at the heading stage and seven days after full heading. This treatment increased ratoon season yield by 6.45%, primarily due to enhanced grain filling rate (GF) and spikelets per panicle (SP). Processing quality was significantly improved; milled rice rate (MR) increased by 5.59–6.24% in FLYX1 and 3.38–3.52% in JLYHZ, while appearance quality also improved, with chalky grain rate (CGR) decreasing by 21.51–22.93% in FLYX1 and 14.50–14.53% in JLYHZ. These improvements were closely associated with elevated protein content and increased accumulation of selenomethionine (SM). Notably, FLYX1 exhibited higher efficiency in converting selenium to organic forms, whereas JLYHZ showed a greater accumulation of inorganic selenium, highlighting genotype-specific responses. This study confirmed that the foliar application of EDTA-Se during key growth phases of rice during the main season can synergistically optimize yield and quality in ratoon rice while achieving Se biofortification and providing a theoretical basis and technical support for improving the quality and efficiency of ratoon rice, as well as producing Se-enriched ratoon rice.