A flexible sealing water hammer for driving a pile in water comprises a ventilating pipe, a hydraulic cylinder support, a water hammer cylinder, a guide block, a flexible sealing cabin, an annular rib, an anvil block, a hydraulic cylinder, a flexible lifting chain, a shock absorption cushion and a hammer head. The 'water hammer'effect in the fluid mechanics is applied to a deep water pile driving device, and flexible systems including the flexible sealing cabin, the flexible lifting chain and the shock absorption cushion are ingenuously adopted. By means of the application of the flexible sealing cabin, the problem of motive sealing between the hammer head and the water hammer cylinder is solved, and manufacturing cost is greatly reduced. Meanwhile, the flexible sealing water hammer has the advantages of being low in energy consumption, low in noise, green, environmentally friendly and the like. Therefore, the flexible sealing water hammer has wide application prospects.