Alternating freezing and thawing is a critical factor associated with soil structure change and accelerates soil erosion in the black soil region of Northeast China. Based on the soils sampled from fields of the black soil region, the effects of freeze-thaw cycles on soil structure at different soil depths (0-40 cm, 40-80 cm, 120-160 cm) and size scales (field core sampling scale of seasonal freeze-thaw cycles, computerized tomography [CT] scale of artificial freeze-thaw cycles, and scanning electron microscope [SEM] scale of artificial freeze-thaw cycles) were studied. We measured and analyzed the hydro-physical properties, percentage of aggregate disruption (PAD), pore number, pore area, pore roundness, and Feret diameter of pores in the field and lab by using CT and SEM methods. Results showed that: freeze and thaw alternation affected black soil structure from different soil depths and different size scales both in seasonal field condition and artificial freeze and thaw cycles condition. At the scale of seasonal freeze-thaw cycles, bulk density of top soil (0-40 cm) increased, total porosity decreased significantly, with non capillary porosity decreasing dramatically. Water holding capacity decreased consequently(P < 0.05). Within the soil depth of 40-80 cm, bulk density and porosity did not change significantly, but PAD increased by 40.97%(P < 0.05)resulting in weak erosion resistance. Hydro-physical properties and aggregate breakdown characterization of soils in the depth range of 120-160 cm were not changed significantly by seasonal freeze and thaw cycles. At the size scale of CT, the alternation did not change the characterization of macro pores in 0-40 cm but significantly reduced the average pore area, roundness and diameter after freeze and thaw cycles. While the average area and diameter decreased significantly in the 40-80 cm depth, this might result in poor infiltration and water movement to the subsoil. Pore area of 1-2 mm and > 5 mm decreased 9.58% and 42.19% (P < 0.05), respectively. Structure of soils from 120-160 cm underwent by artificial freeze-thaw cycles showed similar results as field scale did, were not affected significantly by alternate artificial freeze and thaw cycles. The number of pores with diameter between 1 and 2 mm was predominant the pore size distribution through three soil depths. At the scale of SEM, the roughness of the soil surface and alveolate cells were significantly increased; we also observed micro-aggregate displacement and rearrangement, and disruption of the pore walls. Integrating electron spectroscopy results of 40-80 cm depths, carbon and calcium did not change after 6 freezing and thawing cycles, but oxygen group elements decreased. Magnesium, silicon, aluminum, potassium and iron elements increased to different degrees, and the total increment equaled to the decrease quantity of oxygen group element. The packing arrangement of oxygen group elements and metallic oxide are the key factors to determine the type and surface chemistry of soil clay minerals, so the amount of change in oxygen group and other elements gives indirect evidence that freeze and thaw cycles can affect soil microstructure. But to determine whether or not freeze and thaw cycles would change the crystal lattice structure of clay minerals, further research will be needed and must be approached from the view of soil chemistry and minerology.