Potato variety Hezuo–88 was used in pot experiment to compare the effects of different cytokinin-producing bacteria on agrochemical, physiological and biochemical characteristics of potato seedling under water deficit by adding Bacillus megaterium solution and Bacillus subtilis solution to soil combined with deficit irrigation. The results showed that water use efficiency and drought resistance of potato were improved significantly after adding cytokinin-producing bacteria compared to the control. The root length, root fresh weight, root activity and root dry matter storage of potato in the treatment added with Bacillus subtilis were higher than those in the treatment added with Bacillus megaterium.