A method for preparing high transparent low acyl gellan gum from fermentation broth is provided, in which two-stage filtrations are carried out on deacylated gellan gum fermentation broth by using diatomite and/or perlite with different particle sizes as filter aid and filter media. The obtained product has high gel transparency and low content of metal ions. The method also has the advantages of simple pretreatment of fermentation broth, high impurities removal efficiency, simple operation, and easy to be industrialized.