Consumers prefer high-quality organic agricultural products, but most organic farmers use conventional seeds. Therefore, it is necessary to establish an organic seed production technology for organic vegetable cultivation which will meet international organic standards. In this study, the effects of low temperature treatment and seedling size on flower bud differentiation and planting were investigated for the production of indigenous organic root vegetables seeds, radish, turnip, and beet. Radishes were bolted in large seedlings which were cold treated for 4 weeks after 16 days of transplantation. Turnips were bolted in small seedlings which were cold treated for 2 or 4 weeks after 28 days of transplantation. Beets were bolted in small seedlings which were cold treated for 4 weeks, 23 days after planting. It was found that small size radish seedlings were not affected by the 4 weeks low-temperature treatment, but for turnips and beets, smaller seedlings rapidly bolted as compared to larger seedlings which were treated for 2 or 4 weeks. Based on these results, it could be inferred that it is possible to increase the seed production yield of radish, turnip, and beet as well as predicting the planting time. These findings could be used as basic data to determine the appropriate seedling size and cold-treatment time.