The invention discloses application of soybean phosphatase GmWIN2 and a coding gene thereof to regulation of the seed output of plants. Specifically, the invention provides application a protein (i.e., GmWIN2) composed of an amino acid sequence as shown in sequence 2 in a sequence table to a1) increase of the seed output of plants or to a2) breeding of plant varieties with increased seed output. Experimental results prove that the soybean protein GmWIN2 and the coding gene thereof are related to the seed weight of plants and can increase the seed output of plants after overexpression; and the gene is of critical theoretical and practical significance to increase of crop output, especially to increase of the thousand seed weight/hundred seed weight of plant seeds like soybeans and cultivation of high-yield varieties.