Soil ameliorants can improve soil physico-chemical properties and activate microbial communities in saline-sodic soils. However, there has been less focus on how aggregate fractions affect soil microbial communities under different ameliorant applications. Here, we used the phospholipid fatty acid (PLFA) analysis to explore the effects of soil ameliorants on microbial communities within mega-aggregates (diameter of > 2 mm, ME), macro-aggregates (diameter of 0.25-2 mm, MA), and micro-aggregates (diameter of < 0.25 mm, MI), based on an 8-year rice (Oryza saliva L.) field experiment. The five treatments included CK, non-amended control; SS, amended with sandy soil; DG, amended with desulfurization gypsum; FM, amended with farm manure; and M, amended with a mixture of sandy soil, desulfurization gypsum, and farm manure. Relative to the CK treatment, the SS, DG, FM, and M treatments significantly decreased the soil pH and electrical conductivity and significantly increased the soil organic carbon (SOC) content of the MI, while the FM and M treatments also significantly improved the SOC content of the MA and ME. Irrespective of the ameliorant used, the absolute abundance of total PLFAs and most microbial groups generally varied with the SOC content as follows: MA > ME > MI. Meanwhile, the proportional abundance of arbuscular mycorrhizal fungi (AMF) varied between different aggregate fractions as follows: ME > MA > MI. Additionally, the DG treatment significantly enhanced the soil aggregate stability by increasing the AMF abundance, AMF/saprotrophic fungi ratio, and SOC content of the ML Furthermore, soil microbial groups were highly correlated with soil SOC (P < 0.001), C/N ratio (P < 0.001), pH (P < 0.01), total nitrogen (P < 0.01), and the proportion of aggregates with a > 0.25 mm diameter (P < 0.05). In conclusion, desulfurization gypsum is more effective for improving the properties of saline-sodic soils in the western Songnen Plain.