The invention discloses a method for preparing fermented soybeans in water. The method comprises the specific steps of step one, raw material treatment: after soybeans are soaked by warm water, steaming is performed for 9-15 min under pressurization of 0.15 Mpa; step two, fermented soya bean yeast cultivation; step three, fermentation: during the fermentation period, stirring is performed slightly every 12 h; step four, pH adjustment: 8-10 lemon slices are placed on the surfaces of the fermented soybeans in water, warm water with the temperature of 30 EDG C to 35 DEG C is sprayed to the lemon slices uniformly by a watering pot, the spraying amount of the warm water is 0.5 kg, the lemon slices are covered and placed for 1 h after spraying, and the lemon slices are taken out; step five, seasoning: 40 g of pepper is added, and the mixture is stirred uniformly; step six, sterilization and filling: the mixture is heated to 90 DEG C to 93 DEG C, the temperature is kept for 20 min, and filling is performed while the mixture is hot. According to the method for preparing the fermented soybeans in water, complete appearances of the soybeans can be kept, the processing time is shortened, the phenomena of rancidity and stinking are avoided, and the expiration date of the fermented soybeans in water is prolonged.