The invention provides a processing method for an amino acid fermentation wort. The method comprises using supersonic wave to perform denaturation processing on thalli in the amino acid fermentation wort and then performing solid-liquid separation. By utilizing the provided method to process the amino acid fermentation wort, the obtained fermentation clear liquid has the turbidity close to the turbidity of a fermentation clear liquid obtained by utilizing a filter membrane with good permeability. The provided method is capable of effectively removing thalli in the amino acid fermentation wort. Also the provided method does not need to perform acid adjusting, temperature adjusting and filtration on the fermentation wort, the operation process is simplified, and the cost investment is reduced. Additionally, the employed supersonic wave does not harm to environment, and the method is relatively energy-saving and environment-friendly, compared with the prior art generating a large amount of organics-abundant wastewater during cleaning of the filter membrane.