To investigate the influence of bio-organic fertilizer on the water-salt dynamics and crop yield of different saline soils(greenhouse secondary saline soil(NS)and coastal saline soil(S)), the pot experiment was adopted to study the effects of fertilization regimes on the soil moisture content, soil electric conductivity(EC), soil salt composition, crop yield and water use efficiency of irrigation. The following treatments were applied: controlling without fertilization(CK), chemical fertilizer(C), bio-organic fertilizer(O), bio-organic fertilizer combined with chemical fertilizer(CO, bio-organic fertilizer: chemical fertilizer=1∶1). The results showed that: (a)Compared to C, O and CO can improve the soil water content inboth types of saline soils. (b)Soil salt, indicated by the soil electric conductivity, was controlled well by O and CO treatment. (c)Compared with NS-C, the total amount of soil salt ions in NS-O and NS-CO decreased by 23. 63% and 15. 60%, respectively. (d)Compared with S-C, the total amount of soil salt ions in S-O and S-CO decreased by 22. 34% and 10. 32%, respectively. (e)After the tomato harvesting, the proportion of NO^-₃ and SO^2-₄ in the soil salinity decreased in NS, while the proportion of Na⁺, K⁺ and Cl^- decreased in S. (f)O was the most favorable for soil microbial growth, followed by CO. The yield of tomato treated with CO in the secondary saline soil was the highest, and the yield increased by 165. 5% compared with O. (g)The application of bio-organic fertilizer could improve the crop yield and irrigation water use efficiency of S, and the chemical fertilizer will result in the crop failure. (h)The application of chemical fertilizer can improve the crop yield on saline soil, and irrigation water use efficiency of the bio-organic fertilizer treatment is higher than other treatments.