In this study, plate transparent circle by Davis method was introduce firstly screening α-Rhamnosidase high-yield strain. The spore-sprouted Aspergillus niger 8-hour were mutagenized by ethyl methane sulphonate and pre-screened via transparent circle. 11% mutants yield 40% higher of α-rhamnosidase than the original strain. A high-yield strain, T-226 with the highest α-rhamnosidase activity of 373.4 U/mL was finally selected from these potential high-yield mutants after rescreened by shake flask fermentation twice. When the T-226 strain was fermented in 5 L bioreactor, the enzyme activity could reach to 631.9 U/mL after 84 h. Thus, the established screening method is highly efficient to isolate α-rhamnosidase high-yield mutant of A. niger.