Carbonaceous slate inevitably possesses microscopic pores, microcracks, cleavages, and bedding planes in complex geoenvironment during the diagenesis processes. The microstructure of carbonaceous slate changes apparently under the effects of underground water infiltration, tectonic stress, and engineering disturbance, which induces the large deformation of rock mass and influences the stability of geotechnical engineering projects. To investigate the microstructure characteristics and reveal deformation mechanisms of carbonaceous slate under the influence of water pressure and stress, the variations of the pore size distribution(PSD), connectivity of pores, and porosity of samples during water injection and triaxial compression were studied using multiple methods. The results indicated that voids include plate-like micropores and microcracks, which are discontinuous without external stress. The micropores with a size of less than 1 μm dominate in number. The flaky particles were extruded and bent at a confining pressure, which caused the intermediate pores to form and altered the PSD of the samples. Hence, the connectivity dramatically improved and resulted in increased permeability. Water with dissolved clay minerals and small particles could move between micropores and microcracks during the water injection process. The elastic deformation of the particles recovered, and the intermediate pores disappeared when the imbalanced forces on two sides of the particles were narrowed. Pore water pressure affected the effective stress state and decreased the cohesion and stiffness of the rock. In the lower stress state, the porosity had a certain range of decrease (about 0.2%) mainly due to micropore compression, while the microcrack sprouted and expanded with the increase of compressive stress, resulting in the extension of porosity. The interaction of the stress and water seepage on the slate reduced the rock strength and favored the deformation, leading to a large macrodeformation of the soft rock in the long run.