Organic farming is a cultivation practice with a lower environmental burden than conventional farming. The low yield and the difficulty of weed control in organic farming can be resolved by developing new suitable cultivars. This study investigated the adaptability of Monster Rice 2 (MR2), a new rice line with extra-long culms and high fertilizer use efficiency, to the three aspects of organic farming: growth under green manure (GM) application, weed competitiveness, and deepwater avoidance by comparing it with a semidwarf cultivar, Takanari. In GM application, the above-ground biomass of MR2 at the heading stage was marginally higher than that of Takanari due to a higher net assimilation rate. Although MR2 did not have higher weed competitiveness, it had a better survival rate and growth than Takanari under 20 cm of water in the early growth stage, when most weeds are typically exterminated. These MR2 properties are partially attributable to SD1, an allele that promotes shoot elongation, based on the results that a near-isogenic line of SD1 showed slightly higher growth in GM application and significantly higher deepwater avoidance than Takanari. Our results suggest that long-culm rice has notable future utility and that MR2 could serve as a prototype breeding material in organic farming.