The invention discloses a protein GsMIOX2 related to plant stress resistance as well as encoding genes and application of the protein GsMIOX2. The protein GsMIOX2 is selected from a, b or c, wherein a is a protein of which the amino acid sequence is shown as the sequence 2; b is a fused protein obtained by connecting labels at the N terminal and/or C terminal of the protein shown as the sequence 2; c is a protein with the same function and obtained by conducting substitution, deletion and/or addition of one or more amino acid residues on the amino acid sequence shown as the sequence 2. Experiments prove that when the genes are over-expressed into arabidopsis thaliana, the tolerance to alkali stress in the germination period and the seedling formation period of arabidopsis thaliana can be improved, so that the GsMIOX2 protein can lay a foundation for cultivation of alkali-resistant transgenic plants.