Soybean red crown rot (RCR), caused by the soil-borne fungus Calonectria ilicicola, significantly reduces soybean yield and quality. A hypovirulent strain of C. ilicicola, designated UH2-1A, was obtained by repeated subculturing of the virulent strain UH2-1. UH2-1A exhibited significantly reduced pathogenicity after 20 and 40 subcultures, with RCR symptom scores of 0.8 and 1.0, respectively, compared to 3.0 and 4.0 for UH2-1. No differences in growth rate or direct antagonistic effects were observed between UH2-1A and UH2-1. Notably, incorporating UH2-1A into the UH2-1 inoculum mixture significantly reduced the RCR incidence at UH2-1A/UH2-1 ratios of ≥ 1.0 in greenhouse experiments. The suppressive effect of UH2-1A was also observed against four additional virulent C. ilicicola strains, suggesting broad control potential. These results highlight UH2-1A as a promising biological control agent for soybean RCR and provide an effective method for generating hypovirulent pathogen strains to control diseases caused by intraspecific pathogens.