The invention relates to a preparation method of 2,6-difluorobenzamide by utilizing rhodococcus ruber. The method comprises the following steps: (1) fermentation and culture of seeds; (2) preparation of rhodococcus ruber suspension fluid; (3) conversion of 2,6-difluorobenzonitrile; (4) preparation of finished products. The invention provides a preparation method of 2,6-difluorobenzamide by utilizing rhodococcus ruber to convert 2,6-difluorobenzonitrile into 2,6-difluorobenzamide. The microorganism conversion method has a very high catalytic efficiency, increases the substrate conversion rate, under a material concentration of 3.5 mol/L, the 2,6-difluorobentrinile conversion rate is as high as 100%, the 2,6-difluorobenamide selectivity is 100%, and no by product 2,6- difluorobenzoic acid is generated. The separation and purification technology of target product is simplified, and the method has the advantages of mild reaction conditions, low requirements on equipment, and easy application to production.