For backfill projects in seasonally frozen regions, freeze-thaw and compaction are two critical factors that affect engineering safety by changing the soil structure. This study investigated the effects of freeze-thaw cycles on the microstructure characteristics of saline soil with different compaction degrees using mercury intrusion porosimetry (MIP), scanning electron microscopy (SEM), and laser particle size analysis (LPSA). The compacted soil samples show a bimodal pore size distribution (PSD). With an increase in the freeze-thaw cycles, the volume of intra-aggregate pores (<4 μm) gradually decreases, while that of inter-aggregate pores (>4 μm) varies with the density of soil samples. Furthermore, compaction has a decisive effect on the volume of inter-aggregate pores. Under the effect of freeze-thaw cycles, the void ratio of the low-density soil sample decreases, and the soil structure gradually becomes denser, showing thaw settlement deformation. However, in the high-density soil sample, the void ratio increases and the soil structure becomes loose, showing frost heaving deformation. Moreover, the freeze-thaw cycle also leads to the breakage of coarse particles and the aggregation of fine particles. Correspondingly, the soil structure type changes from a flocculent structure to a granular stacked structure and then to a cemented-aggregated structure. After 60 freeze-thaw cycles, the cracks are penetrated and the water migration channels are formed, the soil structures all reach a new equilibrium state. Meanwhile, the void ratios of different compacted soil samples are close to the same residual value. Test results suggest that there may be an optimal compaction degree between 90% and 95%, where the soil microstructure is least affected by freeze-thaw cycles. This study may provide theoretical guidance for the construction of backfill engineering projects in seasonally frozen regions from a micro-perspective. • The pore size distribution (PSD) of compacted soil samples is bimodal. • The freeze-thaw cycle is ...