In order to ascertain the impacts of microorganism (bacillus subtilis) on soil improvement and water movement in saline alkali soil, a laboratory 1D infiltration experiment of brackish water with different concentrations (0 g/L, 1 g/L, 2 g/L, 3 g/L and 4 g/L) was conducted. The results showed that, bacillus subtilis reduced the infiltration capacity of the soil significantly, and slowed down the water flow. Compared with the control, the cumulative infiltration and the final wetting front distance were significantly decreased in soil with bacillus subtilis. The reduction in the cumulative infiltration was up to 40.97% under the brackish water concentration of 2 g/L. The wetting front distance showed the similar results as infiltration. Then, Philip and Kostiakov infiltration model were used, and the fitting result showed that the imbibition rate S of Philip formula was less than that in the corresponding control groups. This suggested the diminished solid water absorbing ability of capillary force might be due to the viscosity property improvement made by bacillus subtilis. The experience coefficient K of Kostiakov formula was smaller than the control, which indicated that the initial infiltration rate of bacillus subtilis contained solid was lower. Nevertheless, the empirical exponential β was greater than the control, demonstrating that the containing solid capacity of bacillus subtilis was fading with the increasing infiltration time. After the infiltration of brackish water, the soil with bacillus subtilis showed a better aggregate structure, which could significantly improve the ventilation and water holding capacity. Soil water characteristic curve showed that, with the same moisture content and concentration, the water suction of the bacillus subtilis containing solid was stronger than the corresponding control, with more reduced matrix potential, which indicated that bacillus subtilis increase the water holding capacity and inhibit the water evaporation and infiltration. Finally, the water characteristic curve was fitted using van Genuchten model. In this formula, the soil residual water content, saturated water content and coefficient associated with intake value increased, and shape coefficient decreased. In conclusion, bacillus subtilis can improve the solid structure effectively and reduce solid infiltration. This study could provide a theoretical support for the microorganism application in soil improvement.