The application of biochar (BC) can rapidly improve soil physicochemical properties and affect microbial community composition, thereby restoring and enhancing soil ecological functions. However, it is not clear how biochar affects the structural characteristics of soil microbial communities in degraded saline wetlands. In this study, the treatments included control (no biochar, CK), low-level biochar (0.5%, 1% and 2% biochar was added according to the proportion of biochar with soil, LK) and high-level biochar (5%, 10% and 20% biochar was added according to the proportion of biochar with soil, HK). The phospholipid fatty acids (PLFA) profiles and the main drivers of the changes in soil microorganisms in response to biochar addition were investigated for one growth season. The results showed that the microbial community structure changed in response to the addition of biochar in the short-term. Biochar inhibited the PLFA of all microorganisms except for fungi under the low level of addition, but increased the PLFA of all microorganisms except for protozoa at the high level of addition (HK) with about 50% of increase on bacteria and fungi. Species structure of the microbial community did not change significantly under the different biochar additions, and the diversity, dominance and evenness of the microbial community did not differ significantly among the three treatments. Biochar addition changed the nutrient concentrations in the soil, with biochar addition did not significantly alter soil organic carbon (SOC), but increased dissolve organic carbon (DOC) content. The DOC showed significant positive correlations with Gram-positive (G+), Gram-negative (G−) and anaerobic bacteria (Ana), but negative correlations with fungi (Fun). Future studies should focus on the long-term change of microbial community structure under biochar addition.