The invention provides a method for achieving separated layer water distribution by pressure pulse, and belongs to the field of oil and gas. According to the invention, separated layer water distribution is achieved by a wellhead pressure pulse program-controlled generator and a separated layer water injection string which is equipped with an intelligent water distributor. Through the adoption of the method provided by the invention, a separated layer water distribution task can be wirelessly finished in a remotely controlled way without traditional tripping and blending, so that working time and construction cost are saved; and the method provided by the invention is an efficient and advanced separated layer water distribution method with high success rate. Meanwhile, as the wellhead pressure pulse program-controlled generator is used for generating negative pressure pulse, the method provided by the invention has the advantage that separated layer water distribution effects of three layers can be finished within half an hour without stopping a pump, being assisted by other construction operation equipment and using high pressure water as a pressure source; furthermore, the efficiency and the success rate in the prior art are further increased, and the construction cost in the prior art is further reduced.