The invention discloses a waterlogging preventing method and a system thereof for realizing the orderly water drainage in cities. The waterlogging preventing method is that water flow spiral movement generating devices are mounted at water outlets of water collecting wells of underground pipe networks, and the vortex generating coefficient of the water flow spiral movement generating device which is mounted at the water outlet of the water collecting well at a high position is higher than that of the water flow spiral movement generating device which is mounted at the water outlet of the water collecting well at a high position. The system of the waterlogging preventing method for realizing the orderly water drainage in the cities comprises underground pipe networks for cities, and water collecting wells which are communicated with the underground pipe networks, wherein water flow spiral movement generating devices are mounted at the water outlets of the water collecting wells; the water flow spiral movement generating devices are volute casings, or casing structures which are provided with tangential water inlets, axial water outlets and hollow inner cavities and are in circular truncated cone shapes, cylindrical shapes, inclined circular truncated cone shapes or inclined cylindrical shapes. The method and the system thereof can be used for effectively reducing the equivalent flow passing area of pipelines at the water outlets of the water collecting wells at high-elevation regions and the water flow speed of the inner parts of the pipelines.