The invention relates to a special hydroponics suitable for root system culture of Agrobacterium rhizogenes and its application, the device comprising a tank, a plant holder, wherein the plant holder comprises a vertical plate support, a clamping plate, and a plate-mounted frame body provided with a height adjustment groove and a chute provided with a combined upper-layer holding plate, a chute sealing strip and a light-shielding plate, the upper deck being provided with a plant gripping hole, the lower holding plate and the shading plate which are provided with corresponding root and stem holes. The tank is a rectangular box with a net length corresponding to the plant holder. The net width is an integral multiple of the width of the plant holder. The box contains an independent root zone corresponding to the root hole separated by a divider. The device configuration also includes an oxygen pump, a root pruning bracket and a pouring funnel. The device can be used for root system culture of Agrobacterium rhizogenes transgenic plants.