Ginseng root rot, caused by the soil-borne pathogenic fungi Fusarium solani (Fs) and Cylindrocarpon destructans (Cd), severely impacts the quality of ginseng. Despite economic losses due to ginseng root rot, the use of chemical and biological control agents to prevent this disease is apparently limited. Hence, in this study, we applied biochar to soil and monitored the effect of biochar on ginseng pathogens and diversity of soil microbiome, ultimately observing the effect of biochar on the survival of ginseng. Here we show that biochar exhibited high adsorption capacity toward radicicol and nutrients and increased the pH. This adsorption capacity and increased pH explained that biochar not only delayed conidial germination but also influenced normal mycelial growth of Fs and Cd. Biochar supplementation reduced the density of Fs and Cd in soil by 48% and 63%, respectively, and enriched the bacterial diversity in soil. Moreover, biochar supplementation to soil increased the survival rate of ginseng. The microbiota analyses suggested that biochar is a good candidate to manage ginseng root rot disease in ginseng fields and guaranties sustainable ginseng production.