Through the field plot experiment design control group (CK), organic fertilizer combined with desulfurized gypsum (T1), biochar (T2) and desulfurized gypsum (T3) four treatments, the effects of different improvers on the quantity of soil microorganism, physical and chemical properties and the yield of processing tomatoes were analyzed, and the best improver was determined. The results showed that all amendments could reduce soil EC and pH value, increase soil organic matter, hydrolyzed nitrogen, available phosphorus and available potassium and increase the yield of processing tomatoes. Among them, biochar treatment had the most significant effect on improving the yield of processing tomatoes, which increased by 55.96% compared with CK treatment. The number of bacteria and actinomycetes in the soil of each treatment showed a parabolic change, the maximum values appeared in the flowering and fruiting period, and the number of soil fungi showed a downward trend in the whole growth period. The application of biochar, desulfurized gypsum and organic fertilizer compound with desulfurized gypsum can increase the number of bacteria, actinomycetes and fungi in soil, among which the increase of bacteria and actinomycetes in biochar treatment was the largest, which was 1.6~7.8 times and 2.0~6.1 times higher than that of CK treatment, respectively. The number of bacteria and actinomycetes in topsoil was negatively correlated with soil EC and pH value, and positively correlated with soil organic matter, hydrolyzed nitrogen, available phosphorus and available potassium. The above results showed that the number of soil microorganisms was decreased with the increase of soil salinization degree, which had good positive correlation with most soil nutrients. In addition, the soil with a large number of bacteria and actinomycetes had better physical and chemical properties and higher crop yield, so the number of soil bacteria and actinomycetes can be regarded as an important biological index for evaluating soil health. To sum up, biochar treatment (T2, 22.5t/hm2) was the most beneficial to reduce the EC and pH value of moderate saline alkali soil, promote the growth and reproduction of soil microorganisms, improve soil nutrients and the yield of processing tomatoes.