Wuyiencin is produced by Streptomyces ahygroscopicus var. wuyiensis, which has been widely used in China as an industrially produced biopesticide to control various fungal diseases. Although its mechanism of action, breeding, and fermentation had been extensively characterized, less is known about the regulatory functions that affect its biosynthesis or morphological development. The wysR3 gene of S. ahygroscopicus strain CK-15, a novel member of the DeoR family of regulatory genes, was assessed to determine its function by gene knockdown. Herein, we demonstrate for the first time that DeoR family proteins derived from the same source are likely to be a single branch in a phylogenetic tree and show that wysR3 acts as a repressor for its morphological development without effecting wuyiencin production. We found that the Delta wysR3 strain can grow quickly to reach a plateau stage of maximum biomass at 60 h, which is similar to 12 h faster than the wild-type strain. In the industrial fermentation production process, the Delta wysR3 strain can reduce consumption and save both time and money.