The invention relates to a method for removing salt from an antimicrobial lipopeptide solution in a low temperature refrigeration environment. The method comprises 1, carrying out bacillus amyloliquefaciens fermentation for antimicrobial lipopeptide preparation, filtering the fermentation broth, and removing bacteria so that a clear liquor is obtained, 2, feeding diluted hydrochloric acid into the clear liquor, carrying out standing at a room temperature, and removing a supernatant so that slurry-form fluid is obtained, 3, adding an extractant into the slurry-form fluid, carrying out uniform stirring, carrying out extraction and centrifugation, and carrying out microfiltration by an organic membrane to obtain filtrate, and 4, carrying out crystallization on the filtrate at a temperature of -25 to -10 DEG C, and carrying out microfiltration to remove crystals so that an antimicrobial lipopeptide solution is prepared. In a low temperature refrigeration storage environment, the inorganic salt is fully precipitated from the extraction system, and the organic solution subjected to precipitation and microfiltration does not crystallize in low temperature refrigeration storage so that the problem that impurity salts produced by the existing antimicrobial lipopeptide preparation process are removed difficultly is solved.