In order to research the effects of different concentration of Bacillus megaterium and Bacillus subtilis on physiological characteristics and microbial biomass in rhizosphere soil of potato, random blocks designed pot experiments were conducted by adopted favorita, a kind of potato, as testing material. Experiments respectively treated with 33.33% (T1), 16.67% (T2) and 8.33% (T3) of bacteria agent, and control group (CK, distilled water) were designed. The results showed that treatment of T1, T2 and T3 could improve leaf net photosynthetic rate, activity of superoxide dismutase, peroxidase and catalase in tuber formation stage and tuber expansion stage, as well as in improving tuber yield, water use efficiency, bacteria biomass, fungi and actinomycetes in rhizosphere at harvest stage. The net photosynthesis rate in treatment of T2 were 7.17 μmol/(m2?s) and 6.40 μmol/(m2?s) in tuber formation stage and tuber expansion stage, respectively, higher than that of CK. The tuber dry weight, the water use efficiency and the microbial biomass in rhizosphere soil of T2 was 18.6 g/pot, 1.64 g/kg and 6 877.17 CFU/g, respectively, all higher than that of CK.