The damage to microbial solidified engineering residue by freeze-thaw cycles increases the amount of material prone to wind erosion. Microbial solidification of engineering residue was carried out, and freeze-thaw cycle and indoor wind tunnel tests were conducted on the microbial solidified samples to reveal the interaction mechanism between different numbers of freeze-thaw cycles and the wind erosion degree. The test results showed that the larger the number of freeze-thaw cycles, the greater the mass loss of the microbial solidified engineering residue sample due to wind erosion and the lower the surface strength and surface thickness of the sample. However, the surface strength and surface thickness were relatively stable after more than 7 freeze-thaw cycles. The mass loss of the sample was 13 g after 9 freeze-thaw cycles at the maximum wind speed (15 m/s), higher than that of the sample exposed to no freeze-thaw cycles (6 g) but far lower than that of the undisturbed sample (3647 g). The results indicated that the microbial solidified engineering residue had high freeze-thaw resistance. The microbial solidified engineering residue was analyzed by computed tomography (CT) before and after the freeze-thaw cycles, and three-dimensional reconstruction was performed using digital image processing. The microstructure analysis showed that the freeze-thaw cycles did not change the content and spatial distribution of the microbial solidified products but reduced the ability to cement the microbial solidified products and the soil particles. The calcium carbonate inside the hard shell became more fragmented, the equivalent radius of the crystals and the stability of the hard shell decreased, and the porosity increased. However, the microbial solidified engineering residue exhibited high resistance to wind erosion and freeze-thaw cycles.