In this work, the natural indigo production process from Polygonum tinctorium was balanced based on the traditional Niram method in Korea. A standard procedure was determined considering the conditions of indican extraction from plant material, the amount of alkali for precipitation, storage of extract, etc. The effect of experimental conditions on the yield of crude dye was investigated. The contents of indigo and indirubin of the crude dyes were analyzed by HPLC. Increase of the amount of crude dye was observed within 1-2.5 days of extraction time. Longer extraction beyond 2.5 days resulted in a slight decrease in the amount of crude dye. There was no consistency in terms of indigo content depending on extraction pH. We found that the storage of extract or harvested plants affected adversely to dye yield and dye quality. Based on the lab scale extraction, large scale extraction was performed for 2-2.5 days in water and 2.0-2.5 g/L of $Ca(OH)_2$ was applied for precipitation of indigo dye. We obtained natural indigo dye containing about 15% of pure indigo in scale-up production using whole plant except root.