The invention relates to the technical field of hydroponic culture, in particular to a hydroponic culture method of hydrocotyle verticillata. The method includes the steps that firstly, soil on a root system of hydrocotyle verticillata needing hydroponic culture is cleared away, all old roots and branch roots are cut off, and the length of a reserved main root is smaller than 1 cm; secondly, the root of the hydrocotyle verticillata is placed in a potassium permanganate aqueous solution to be soaked for 10-15 min and then placed in a shady and cool environment for 2-3 hours; thirdly, a culture substrate is placed in a hydroponic culture container, and then a rooting solution and a nutritional source are added, wherein the rooting solution is prepared from a vitamin B12 injection and water in the volume ratio of 1:(2000-5000), and the culture substrate is prepared from ceramsite and charcoal; fourthly, water is replaced every 12-16 days, during each time of water replacement, one third of water in the hydroponic culture container is poured out and then clean water is supplemented, a nutritional solution is added in the second day after each time of water replacement, and the container is irradiated by sunlight for 4-6 hours every day. By using the culture method, the hydrocotyle verticillata can grow vigorously, and the flourished state can be kept for a long time.