The invention relates to the field of plant cultivating, and particularly discloses a water culture method of a woody plant. The water culture method of the woody plant comprises the following steps of cleaning, root pruning, disinfecting, water controlling, primary root promoting, field planting, secondary root promoting and conservation. According to the water culture method, growth conditions of the woody plant are fully considered, twice root promoting is conducted on the woody plant, and therefore less damage is caused to root fibers of the plant, and the survival rate of the woody plant is increased effectively. According to the water culture method, the woody plant has access to the market by being used as an ornamental plant bonsai in a water culture mode, and the situations that during soil culture, fertilization is conducted frequently, and the environment is affected because bacteria and peculiar smell are produced during soil replacement and watering are avoided. The woody plant cultured with the water culture method grows robustly and trimly, has deep green leaf colors and is bright in color, more large flowers are produced, the flowering period is long, and the ornamental effect and artistic value of the bonsai are greatly improved.