The invention discloses a fungal alpha-amylase-containing beer complex enzyme and a preparation method thereof, belonging to the field of enzyme preparation processing. The high-activity fungal alpha-amylase and other food grade enzyme preparations, plant extracts, antioxidants, protective agents, activating agents and the like can be scientifically compounded by taking concentrated maltase and concentrated malt juice powder as main raw materials; the prepared beer complex enzyme is complete in proteases, high in enzyme activity, difficult to deactivate, mellow in malt aroma, and capable of providing abundant nitrogen source for malt juice, wherein the activity of fungal alpha-amylase in fermenting liquor during the preparation of fungal alpha-amylase is 17000-21000 U/mL. The complex enzyme can be stored for 12 months under the conditions of 0DEG C and 40DEG C, the single enzyme activity loss in the complex enzyme are respectively 0.50% and 0.72%, the enzyme deactivation caused by environment change, and inappropriate operation methods during packaging, storage, transportation, use and the like can be effectively prevented, especially the enzyme deactivation caused by high temperature can be prevented.