The micro pores in loess show regional variation in structure on the Loess Plateau and greatly influence the physical properties and macro behaviors of loess. In this study, the 3D microstructures of Malan loess from Lanzhou (LZ), Qingyang (QY), Hengshan (HS) and Jingyang (JY) were established based on μ-CT scanning, and the corresponding microstructural parameters were compared and analyzed quantitatively. The results indicate that the LZ and HS loess both show overall homogeneous structures with dominant inter-particle pores, while the QY and JY loess have more intra-aggregate and constricted pores. Overall, the LZ loess has the largest pore size, followed by the JY loess, QY loess and HS loess, which is consistent with the throat sizes of the four loess samples. The average coordination numbers (CNs) of the LZ and HS loess are lower than those of the QY and JY loess, while the throat lengths of the former two loess are larger than those of the latter two loess. Analysis of the correlation between the micropore parameters and macro behaviors of the loess suggests that the void ratio is the precondition for loess collapse, but it shows weak relevance to collapsibility; meanwhile, the size of pores contributing to the major pore space presents a strong positive correlation. The throat length representing the pore structure is more closely related to loess permeability compared with the void ratio, average CN and throat size.