A method of manufacturing soup with fermented soybeans(Cheongkukjang), fermented soybean powder and fermented soybean pills by fermenting soybeans and shiitake(Lentinus edodes) with Bacillus subtilis is provided to remove characteristic off-flavor of fermented soybeans and improve medicinal value of shiitake. First, 6 to 12% by weight of dried shiitake or 24 to 36% by weight of fresh shiitake is ground to 80 to 120 meshed, steamed, mixed with soybeans and mugwort extract, inoculated with Bacillus subtilis and fermented at 28 to 30deg.C for 24 to 36hr in a fermentation room which is constructed with loess mud yellow soil. The obtained soup with fermented soybeans is dried and ground to obtain fermented soybean powder, or mixed with 2 to 5% by weight of glutinous rice flour to obtain a fermented soybean pill. The soybeans are obtained by boiling soybeans and soaking in loess water(Jijangsu).