The invention discloses a water injection system of a deep roadway and a water injection method thereof. The system comprises water injection pipes, hole sealing devices, humidity sensors, a humidity alertor and a water supply device. The humidity sensors are arranged in water injection drilled holes of the roadway and located on a plastic circle layer in surrounding rock circle layers of the roadway. One ends of the humidity sensors are located on the boundary of the elastic circle layer and the plastic circle layer in the surrounding rock circle layers. The bottoms of the water injection drilled holes are located in the primary rock stress circle layer in the surrounding rock circle layers, and the distance between each water injection drilled hole and the boundary of the elastic circle layer and the primary rock stress circle layer is within 20 cm. The water injection pipes are arranged in the water injection drilled holes and penetrate through the humidity sensors, and the ends of the water injection pipes are arranged between the bottoms of the water injection drilled holes and the boundary of the elastic circle layer and the primary rock stress circle layer. The hole sealing devices are arranged in the water injection drilled holes and located in the elastic circle layer, and one ends of the hole sealing devices are located on the boundary of the elastic circle layer and the primary rock stress circle layer. Through the water injection system, the ends of the water injection pipes are arranged in the specific positions, so that the water injection effect is improved.