The macroscopic properties of loess are significantly controlled by its microstructure. Quantitative analysis of loess microstructure is essential for modeling the microstructure and further incorporating the microstructural effects into geotechnical practice. However, loess has a multi-scale microstructure ranging from nanometer to millimeter scales, and researches at the particle resolution are still inadequate. This study systematically investigates the micrometer-scale microstructure of loess from Jingyang, China, via X-ray computed tomography and the image segmentation method that was explored for loess. The statistical analyses of three-dimensional (3D) microstructure reveal that the particle size follows the Weibull distribution, and the distributions of pore and pore throat sizes obey the gamma distribution. Most particles are blade-shaped, with a peak length ratio of (1.53–1.64):1.28:1. The particles are oriented in the polar directions but not azimuthally, in a spherical coordinate system, exhibiting a transversely isotropic structure. The quantitative microstructures of the loess and paleosol samples were slightly different irrespective of the large aggregates developed in paleosol sample. Moreover, the representative elementary volume obtained through porosity is also applicable for the analysis of microstructural parameters such as size distribution, shape factor, orientation angle, and pore connectivity. Besides, the two-dimensional (2D) distributions of the particle, pore, and pore throat sizes agree with the 3D distributions, except that the former were marginally smaller. However, the 2D sectional analysis of shape, arrangement, and pore connectivity cannot adequately represent the 3D characteristics.