Loess structure is the physical key factor that determines its stability and consists of macro-pores, loose texture, and water sensitivity. The structural change characteristics and effects of the undisturbed loess before and after water infiltration are studied using mechanical CT and simulation tests in order to study the structural change process within the undisturbed loess caused by water infiltration. The change in particle state is as follows: the peak frequency point of the equivalent diameter of the loess particles after infiltration ranged from 16.75 to 23.76 μm, and the eroded fine particles consisted primarily of fine particles. The smaller loess particles are removed by water infiltration resulting in coarsening of soil particles. The sphericity of the loess particles gradually changes from spherical pores to angular and dendritic pores. The particle inclination angle transitions to a range greater than 70°, and its proportion is approximately 61%. The change in pore structure is as follows: The loess porosity after infiltration increased by approximately 20%, and the increase in the pore area ratio of the mesopores and the macropores was higher than that of the micropores. Additionally, the small pores increased by more than 5 times the original state of the undisturbed loess. The connected pores expanded less than 60% of the initial state to more than 90% after infiltration, thus, increasing the dominant seepage channel of the undisturbed loess. These changes in particle and porosity further increase the water filtration intensity and promote the migration of fine particles (mainly silt particles), linking loess catastrophes and are the leading cause of loess settlement and slope instability. The process of water infiltration into the loess, the mechanism of loess collapsibility, and the influence of salinity on the loess structure and strength are discussed in this study.