The invention discloses protein GsSLAH3 related with stress tolerance of plants and an encoding gene and application thereof. The protein GsSLAH3 is characterized in that a gene GsSLAH3 is obtained by cloning from wild soybean, and is stressed and induced by carbonate to realize up-regulated expression; indicated by tissue positioning and analysis, the gene GsSLAH3 is mainly expressed in tissues of roots, stems, hypocotyls, capsules and the like; after the gene GsSLAH3 is instantaneously expressed in epidermic cells of onion, the fact that a fusion protein fluorescent signal mainly appears in cytomembrane is found; after the gene GsSLAH3 is over-expressed in arabidopsis thaliana, the fact that the tolerance of the arabidopsis thaliana on the stress of the carbonate can be enhanced by the gene GsSLAH3 is found; a study foundation is laid for the culture of a new variety of alkaline-resistant crops, and the important meaning is realized for development and utilization of saline and alkaline land resources.