The invention provides a water plugging pipe column suitable for a small partitioning layer plug bottom water well and a water plugging method. The water plugging pipe column comprises a first oil pipe, a hydraulic releasing tool, a second oil pipe, a locating short section, a third oil pipe, a hydraulic packer, a fourth oil pipe, a long rubber cylinder packer and a screwed plug which are connected in sequence. The water plugging method comprises the steps that the water plugging column goes down to an appointed position in the well, so that the position of the hydraulic packer and an upper partitioning layer correspond, the position of the long rubber cylinder packer and a lower partitioning layer correspond, the upper partitioning layer is placed between an upper oil layer and a middle oil layer, the lower partitioning layer is placed between the middle oil layer and a lower oil layer, liquid is injected into the water plugging pipe column from a well opening and is pressurized to reach a first pressure value, the hydraulic packer and the side wall of the upper partitioning layer are subjected to corresponding setting, the long rubber cylinder packer is set on the side wall of the lower partitioning layer, liquid is continuously injected into the water plugging pipe column from the well opening and is pressurized to reach a second pressure value, so that the upper portion and the lower portion of the hydraulic releasing tool are separated, the upper portion of the tool is taken from the well along with the first oil pipe, and the first pressure value is smaller than the second pressure value.