The invention relates to a method for processing 1,3-propanediol concentrated bacterial liquid. The method comprises the following steps: separating thalli in fermentation liquid through membrane filtration, wherein membrane filtration equipment can select and use fibrous membrane, ceramic membrane or stainless steel membrane; adding water into the concentrated bacterial liquid according to a volume ratio of 1:1 to 20 for dilution; at normal temperature, adding a compound medicament into the diluted bacterial liquid according to a volume ratio of 100:0.2 to 2, and adding an alkaline substance to regulate the pH value to 9-12, wherein the compound medicament is the aqueous solution of ferrous sulphate and polymer ferric sulfate, the mass of the ferrous sulphate is 10 to 30%, the mass of the polymer ferric sulfate is 10 to 30, and the balance is water; then adding one per mill polyacrylamide solution according to a volume ratio of 100:0.1-1; and settling for 5 to 30 min and filtering. The method has the advantages of simple process, easy operation, low treatment cost and good flocculation and settlement effect, which is applicable to the treatment of the production of 1,3-propanediol concentrated bacterial liquid by fermentation method.