The invention discloses a group of HAP3 genes which are derived from rice and are related with stress tolerance, the encoded protein has one of the following amino acid sequences: 1) the SEQ ID No:1, 3 or 5 in a sequence table; 2) the amino acid residue sequence of the SEQ ID No.:1, 3 or 5 in the sequence table is treated with the substitutes, deletes or adds of one to ten amino acid residues andthe derived protein has the effect of regulating the performance of plant stress tolerance. The experiments proves that the transgenic rice of the invention can improve the tolerance of the rice to the high-salt, drought and low-temperature adversity threats and have no apparent impacts on the normal growth and the economic traits of the rice. The protein and the encoded genes of the invention have important theoretical and practical significances on the research of a plant stress tolerance mechanism, the improvement of the plant stress tolerance and the improvement of the related traits, thereby playing an important role in the stress tolerance genetic engineering improvement of plants (particularly cereal crops) and having broad application prospect.