The invention provides a shallow water air-pruning seedling culture method, and belongs to the technical field of plant seed seedling culture. The method includes the steps that a grid tray is additionally arranged at the bottom of a seedling culture pond, a seedling culture tray is placed on the grid tray, plant seeds are sown in holes of the seedling culture tray, and seedling substrates are arranged in the holes of the seedling culture tray; after a nutrient solution is added for the first time, the liquid level of the nutrient solution does not exceed the upper surface of the seedling culture tray, in the seedling culture process, after the liquid level of the nutrient solution is separated from the bottom of the seedling culture tray, water is added when fertilizer needs to be added or seedlings are withered, and the liquid level after water adding is 0.5 cm higher than the bottom of the seedling culture tray. By adopting the method, excessively high seedlings are not likely to occur in the obtained seedlings, no spiral roots are generated, the amount of moss is small in the whole seedling culture process, and the seedling rate is high.