Study on the microscopic structure of saline-alkali soil can reveal the change of its permeability more deeply. In this paper, the relationship between permeability and microstructure of saline-alkali soil with different dry densities and water content in the floodplain of southwestern Shandong Province was studied through freeze-thaw cycles. A comprehensive analysis of soil samples was conducted using particle-size distribution, X-Ray diffraction, Freeze-Thaw cycle test, saturated hydraulic conductivity test and mercury intrusion porosimetry. The poor microstructure of soil is the main factor that leads to the category of micro-permeable soil. The porosity of the local soil was only 6.19–11.51%, and ultra-micropores (< 0.05 µm) and micropores (0.05-2 µm) dominated the pore size distribution. Soil saturated water conductivity was closely related to its microscopic pore size distribution. As the F-T cycles progressed, soil permeability became stronger, with the reason the pore size distribution curve began to shift to the small pores (2–10 µm) and mesopores (10–20 µm), and this effect was the most severe when the freeze-thaw cycle was 15 times. High water content could promote the effects of freeze-thaw cycles on soil permeability and pore size distribution, while the increase of dry density could inhibit these effects. The results of this study provide a theoretical basis for the remediation of saline-alkali soil in the flooded area of Southwest Shandong.