Carbonaceous slate exhibits a significant creep deformation that seriously affects the construction and operation of underground projects. To investigate the microstructural changes characteristics and reveal the microscopic deformation mechanism of the carbonaceous slate during the creep process, multiple methods were performed, including the triaxial creep test, SEM and MIP. The following conclusions were drawn: The rock samples underwent three stages during the creep test: microporosity closure at a low-stress level, material densification at an intermediate stress level, and microcracks emerging and expanding to failure at the high stress. The creep deformation was particularly significant in the first and third processes. The lamellar particles are compressed or bent under stress in parallel and vertical directions, showing the anisotropic properties of deformation. The deformation of the rock sample is related to the angle between the bedding and the orientation of major principal stress, and the effect of the anisotropy decreases with the increased stress level. The sprouting and expansion of microfractures occur at high-stress levels, showing pressure dissolution of mineral particles, migration of very fine particles, and cement damage between lamellar particles. Finally, the horizontal samples formed a combined rupture surface composed of the laminar surface and the fracture surface intersecting it, showing brittle damage, while the vertical samples formed a fracture surface parallel to the laminar surface, showing a ductile damage pattern. Those results could provide the basis for a further understanding of the mechanical properties of carbonaceous slate and the improvement of its creep model and parameters. It was significant for the stability analysis and deformation prediction of engineering structures using numerical simulation.