In this paper, five different contents of Bacillus subtilis (0, 1, 3, 5, 7 g/kg) were setted, aimed to study the effect of B. subtilis on evaporation of soil surface and water and salt distribution in saline-alkali soil. The results showed that: (1) With the application of B. subtilis, the cumulative evaporation and evaporation rate in saline-alkali soil decreased obviously, comparing to that in control soil columns, especially after the initial 2 days. The cumulative evaporation and evaporation rate of soil with different B. subtilis content (0, 1, 3, 5, 7 g/kg) was smaller than that without B. subtilis application, and reached smallest when B. subtilis content was 3 g/kg. In the 41st day after evaporation, the cumulative evaporation of treatments with 1, 3, 5 and 7 g/kg B. subtilis were decreased by 16.63%, 21.39%, 11.26% and 5.96% compared with that in 0 g/kg, and the variations between the treatments were significant (P＜0.05). (2) Both Black and Rose model could fit soil evaporation process well with different B. subtilis contents. For the Black evaporation model, with the increase of B. subtilis contents, evaporation parameter B firstly decreased and then increased compared with the control treatment (P＜0.05). For the Rose evaporation model, with the increase of B. subtilis contents, stable evaporation parameters C and moisture diffusion parameter D firstly decreased and then increased, which were obviously less than the treatment received 0 g/kg B. subtilis (P＜0.05). When the B. subtilis was 3 g/kg, the minimum values of C and D were obtained, which further confirmed that B. subtilis could increase soil water holding capacity. When the B. subtilis content were 1, 3, 5 and 7 g/kg, the water contents were greater than that in the control. (3) At the depth of 6 cm, the water content in the treatments with B. subtilis of 1, 3, 5 and 7 g/kg increased by 28.24%, 37.40%, 20.00%, 6.87% respectively, compared with that in the control. (4) Soil salt contents were also significantly decreased with the application of B. subtilis. The salt content in the treatments with B. subtilis of 1, 3, 5 and 7 g/kg decreased by 32.26%, 46.89%, 26.34%, 14.65% respectively, compared to that in the control. (5) After applying B. subtilis, the soil residual water content θr, saturated water content θs and coefficient associated with intake value α were all increased and shape coefficient n was decreased in van Genuchten equation. In summary, application of 3 g/kg B. subtilis could inhibit salt and improve soil water holding capacity in saline-alkali.