The invention discloses a domestication method of nostoc and application thereof. The domestication method comprises the following steps of: preparing a specific culture medium; carrying out salt tolerance domestication, nitrogen and phosphorus content reduction domestication, domestication of adaptability to water to be treated, and the like on screened nostoc species; carrying out step-by-step amplification culture; then leading the nostoc species into a saline and alkaline land, wherein the nostoc is propagated in large quantities by utilizing photosynthesis and absorbs and fixes nitrogen and phosphorus elements contained in atmosphere and water sources; and after the nostoc is propagated, draining culture water for the nostoc, wherein the nostoc is deposited in soil and contains a large quantity of elements, i.e. nitrogen, phosphorus, and the like. After primary treatment is carried out by using the domestication method, the nitrogen contained in the soil is increased by 18-21 percent, the phosphorus is increased by 12-14 percent, and full salt content is reduced by 15-18 percent, therefore not only is nutrient element loss caused by a water washing method prevented, but also the hardening of the soil and the secondary pollution to the water sources and environments, which are caused by chemical fertilizer application, are prevented; and in addition, soil fertility is gradually enhanced and soil restoration is accelerated through multi-time treatment, therefore the purpose of improving an ecological environment is finally achieved.