The invention relates to a layer-by-layer acidification and stratified water injection method. The method comprises the following steps in sequence that an acid injection integrated tubular column isput into a casing, pretreatment fluid and respective acid liquor of upper and lower strata are prepared, after the positive circulation of fluid is normal, the positive substitution of the pretreatment fluid is carried out, a 31mm steel ball is dropped into a acidizing single flow valve, and a cement truck forward presses to set a packer; the cement truck continues to boost the pressure, shears ashear pin of an inner sleeve ball seat, and the inner sleeve ball seat falls into an inner coated tubing; lower acid liquor is then sent down a well, flows from a screen and enters into a lower waterinjection layer; another a 48mm soluble ball is dropped into a switch valve for setting, the pretreatment fluid is forward pressed to open an acid liquor channel of a barrel wall of the switch valve,and then upper acid liquor is injected into an upper water injection layer; then the well is closed, and two strata continue to acidify; after the acidification reaction is complete, and the soluble ball is dissolved; and a 40mm sealing steel ball is put in, and water is injected normally after tests of throwing and retrieving and sealing are qualified. According to the method, only one trip is needed, the operation cost is low, a well occupancy period is short, the development cost of an oilfield is reduced, and the environmental benefit is good.