The invention provides a water drainage system and method based on a downward extraction borehole, wherein the method comprises the following steps: tripping a protection casing and a breather pipe in the downward extraction borehole, wherein the breather pipe is communicated with the protection casing; extracting gas in the downward extraction borehole through the protection casing, and monitoring whether the negative pressure in the downward extraction borehole reaches the preset value in a preset period; when the negative pressure reaches the preset value in the preset period, opening the breather pipe and employing the pressure difference of the negative pressure and the outside atmospheric pressure to drain the logged water in the downward extraction borehole through the protection casing. The drainage system and method based on downward extraction borehole provided by the invention solve the technical defect in prior art that the logged water in the downward extraction borehole influences continuous gas extracting.