The invention provides a novel plant strong salt tolerant gene AtNHXS1 acquired through DNA reshuffling technology, and the ionic transport activity of Na+/H+ antiporter protein coded by the gene is stronger than that of wild Na+/H+ antiporter protein ATNHX1. A nucleotide sequence of the gene as shown in SEQ ID NO:1 also comprises genes of the nucleotide sequence of sequence 1 in a sequence tablewith the homology between 70 and 100 percent, or a nucleotide sequence of an amino acid sequence of sequence 2 in a coded sequence table. The new Na+/H+ antiporter has a protein of the amino acid sequence of sequence 2 in the sequence table, protein of the amino acid sequence of the sequence 2 with the homology between 70 and 100 percent, or protein which replaces, deletes or adds one or a plurality of amino acids in the amino acid sequence of the sequence 2 with the same homology. The invention also provides the construction of recombinant vector, the transgenic plant and other methods so asto apply the gene and the protein, thereby cultivating a novel variety of transgenic plant with strong capacity of salt tolerance or other improved biologic characters.