The invention discloses a repairing method of microorganism in contaminated soil of chromium slag storage yard, comprising the steps of selecting Pannonibacter phragmitetus BB single bacterium, dropping the single bacterium in a liquid culture medium containing Cr (VI) of 50-250mg / L for culturing until Cr (VI) is not detected in the culture solution, selecting strains in a bottle for transferring, gradually improving the Cr (VI) concentration for gradient domestication, adding the domesticated Pannonibacter phragmitetus BB lysate in the contaminated soil, and culturing for 4-5 days at a temperature below 30 DEG C, so as to repair the soil, wherein the amount of the added lysate is that the mass-volume ratio (g: mL) of the soil to the lysate is 1: 2. The invention treats and repairs hexavalent chromium-contaminated soil through the strains with hexavalent chromium reducing capacity, the operation is simple and feasible, the cost is low, and the method is an environment-friendly treatment method.