The field test results have shown that the physical and chemical properties of saline-alkali soil can be significantly improved by adding fly ash-based soil conditioner. However, at present, the improving mechanism of fly ash-based soil conditioner is not clear, and the structural change law of soil particles is not understood. So this work took the typical saline-alkali soil in the Yinbei area of Ningxia Hui Autonomous Region as the research object, studying the microstructure of saline-alkali soil particles under the action of fly ash-based soil conditioner by X-ray diffraction (XRD), infrared spectroscopy (FTIR), specific surface automatic physical adsorption instrument (BET) and scanning electron microscope (SEM). The results showed that the main components of soil minerals did not change, but a new crystal phase calcite was found in the soil after the fly ash-based soil conditioner was added and the pH value of the soil was greatly reduced from 9.01 to 7.66. The infrared absorption of the soil with fly ash-based soil conditioner changed little, but the absorption peaks of Si-O-Si and organic matters were slightly enhanced. The soil microstructure changed greatly with the increase of the conditioner addition since the small soil particles began to aggregate and the soil porosity gradually increased. Taking the 2.5wt% group as an example, its porosity was up to a level of 21.30% after 15 days and 25.29% after 30 days, which was about twice that of the blank control group. The specific surface area of soil particles increased slightly from the initial value of 23.06 m2/g to 25.55 m2/g after 30 days. The above results proved that fly ash-based soil conditioner could not only alleviate the problem of land salinization, but also realized the large-scale consumption of fly ash solid waste.