A method of preparing beta-carotene uses the Flavobacerium aquatile as material bacterium; the method adapts deep fermentation technology. Carbon and nitrogen source as optimal culture, as well as inorganic salt, the temperature 23-34Deg.C, pH5-9, time 2-6days. When the nutrient solution obtains the mycelium by gentrifugalism, extracts mycelium with organic solvent of acetone and after vacuum concentration or further carries on the silica gel column chromatographic analysis the organic solvent, it may prepare beta -carotene products of different content and different use. The method has the character of a broad apply scope, is prone to sweeping production with low cost.