The invention discloses a water turbine generator set rotating part concentricity adjusting method. The method comprises the steps of installing a hydraulic stretcher on a bolt, connecting an oil pipeline, operating a high-pressure oil pump, rotating a nut, observing the reading of a dial indicator, firstly controlling a water turbine shaft to descend by a certain distance, then lifting one side by a corresponding distance, and then lifting the other side; and enabling a lower flange of a generator shaft and an upper flange of the water turbine shaft to be combined at a combining seam, so thatthe central position of the water turbine shaft is changed. According to the adjusting method, operation is flexible, use is easy, measurement data is controllable, existing equipment materials are fully utilized, resource investment is reduced, and the success rate is improved; on the premise of ensuring the construction safety quality, the construction cost is reduced, and the economic benefitsare increased; and repeated disassembling and assembling and repeated jigger checking are not needed in the whole process, so that the working efficiency is effectively improved.