Experiments were conducted to examine the ecophysiological traits of yield and ripening and the genetic backgrounds of these traits in high-yielding semi-dwarf indica rice. Field experiments were performed over four years to examine the yield and growth characteristics of these traits. A large sink size with large numbers of spikelets per panicle and a high ripening ability in the background of a large sink size were found to be two of the major ecophysiological traits that enhance the yield of semidwarf indica. High dry matter productivity after heading was suggested to be linked to a high ripening ability. To determine the genetic backgrounds that control these traits, quantitative trait locus (QTL) analysis was conducted using two different semi-dwarf indica/japonica inbred lines: recombinant inbred lines of Milyang23 (semi-dwarf indica)/Akihikari (japonica), and back-crossed inbred lines of Sasanishiki (japonica)/Habataki (semi-dwarf indica)//Sasanishiki///Sasanishiki. QTLs for larger sink size, higher ripening ability, higher dry matter production, and larger nonstructural carbohydrate (NSC) reserves in leaf sheaths and culms at heading within semi-dwarf indica alleles were detected. The effects of these QTLs probably combine to express the large sink size and high ripening ability traits, resulting in the high yields of the semi-dwarf indica rice varieties.