The invention discloses a parathion-methyl degradation enzyme mutant as well as an encoding gene and application thereof and belongs to the field of construction and application of the parathion-methyl degradation enzyme mutant. The parathion-methyl degradation enzyme mutant with a secretion capacity, which is remarkably increased in yeast supernatant, is screened from a constructed yeast mutant library by adopting a DNA (Deoxyribonucleic Acid) shuffling technology. The invention further discloses a recombinant expression vector and a recombinant host cell, which contain a parathion-methyl degradation enzyme mutant encoding gene. According to the parathion-methyl degradation enzyme mutant disclosed by the invention, the secretion capacity of the parathion-methyl degradation enzyme mutant in the yeast supernatant is remarkably increased, and industrial production requirements can be met; and the parathion-methyl degradation enzyme mutant has an important application prospect in the aspect of degrading organic phosphorus.