The invention discloses a double-water-storage-tank water injection system, a water injection method and a storage medium, and belongs to the technical field of oil field water injection. The double-water-storage-tank water injection system comprises a first water storage tank, a second water storage tank, a first plunger pump, a second plunger pump, a first water conveying pipeline, a second water conveying pipeline, a connecting pipeline, a first valve, a second valve, a third valve, a first flow meter and a second flow meter, and the connecting pipeline connects the first water conveying pipeline with the second water conveying pipeline. During normal water injection, the first water conveying pipeline and the second water conveying pipeline are opened, the connecting pipeline is closed, when the liquid level in the second water storage tank is too high, the connecting pipeline is opened, the first water conveying pipeline is closed, the second water conveying pipeline is kept opened, injected water in the second water storage tank enters the first plunger pump and the second plunger pump at the same time, and accordingly the liquid level height can be rapidly reduced. In addition, part of injected water is subjected to flow dividing through the first plunger pump, excessive injected water is prevented from being injected into an oil pool, and the effect of water injection development is improved.