The invention discloses a soilless culture system with a water level controller. The soilless culture system comprises a liquid supply pool, a water pumping machine, a culture container and the water level controller, wherein the water level controller is used for controlling a power supply of the water pumping machine, the water pumping machine pumps nutrition solution in the liquid supply pool into the culture container, the culture container is provided with a liquid outlet used for flowing back nutrition solution in the culture container back into the liquid supply pool, the water level controller comprises a power supply circuit and a control circuit connected with the power supply circuit, the power supply circuit comprises a transformer and a rectifying circuit, the transformer is connected with a power supply, the rectifying circuit is connected with a secondary winding of the transformer, the control circuit comprises a relay, an NE555 chip, a high-water-level detection line, a middle-water-level detection line and a low-water-level detection line, the relay is used for controlling the power supply of the water pumping machine, the NE555 chip is used for controlling the relay, the high-water-level detection line, the middle-water-level detection line and the low-water-level detection line are arranged in the culture container and are connected with the NE555 chip, the output end of the rectifying circuit is respectively connected with the water-level detection lines, the output end of the rectifying circuit is also connected with a fourth pin and an eighth pin of the NE555 chip, a first pin of the NE555chip is grounded, a third pin of the NE555 chip is connected with a light emitting diode and is grounded, and the relay is connected with a primary winding side of the transformer.