The invention belongs to the field of biochemical engineering, and discloses a method for producing 3,6-dichloropyrimidine-2-carboxylic acid by biocatalysis. In the method, a nitrilase-producing active cell is taken as a biocatalyst, and a substrate 3,6-dichloro-2-cyanopyridine is hydrolyzed into the 3,6-dichloropyrimidine-2-carboxylic acid in a water-organic solvent biphasic system at the temperature of between 15 and 35 DEG C. In the method, biocatalytic reaction is coupled with product separation, so that the toxicity and inhibition effect of the high-concentration substrate and the product on the cell is effectively overcome, and the product is effectively separated; therefore, the method has the advantages of simple operation, mild reaction condition, and suitability for industrialized production.