The invention relates to a method for stratum-by-stratum acidification and stratified water injection for multiple stratums. The method for stratum-by-stratum acidification and stratified water injection for the multiple stratums comprises the following steps: descending an integrated acidification-injection pipe column into a sleeve, after liquid outlet of a direct circulation is normal, carryingout forward displaced injection on a treatment liquid, then pouring a steel ball with a size of 31mm, enabling the steel ball to fall into an acidification check valve, and carrying out forward pressurization by a cement truck to set two packers; continuing to raise a pressure by the cement truck, shearing off a shear pin of an inner sleeve ball seat, and enabling the shear pin to fall into a coating oil pipe; then conveying a lower-stratum acid liquid to be underground, and enabling the lower-stratum acid liquid to flow out from a sieve pipe and enter into a lower water injection stratum; pouring a sealing steel ball with a size of 40mm, and carrying out acid injection on a middle water injection stratum through an intelligent acid injection valve; then pouring a soluble ball with a sizeof 48mm, enabling the soluble ball to fall into a switch valve to set, pressurizing to open an acid liquid channel in the barrel wall of the switch valve, and then injecting an upper-stratum acid liquid into an upper water injection stratum; then closing a well, and continuing to acidify the three stratums; after the acidification reaction is completed, dissolving the soluble ball; and after theintelligent acid injection valve is closed, carrying out a dropping-fishing test and a sealing inspection test, and after the dropping-fishing test and the sealing inspection test are qualified, carrying out normal water injection. According to the method, only one pipe column trip is needed; and the method is low in working cost, short in well occupancy period, capable of reducing the oilfield development cost, and good in environmental benefits.