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A multi-functional true triaxial fluid-structure coupling system was used to conduct water retention and seepage tests of shale under true triaxial loading and unloading stress paths. The stress–strain evolution of shale specimens under different experimental conditions was obtained, and the corresponding deformation and strength were analysed. The evolution and failure characteristics of cracks in shale were obtained by CT scanning images before and after the experiment. The results show that the volumetric strain of shale specimen increases first, then decreases and finally continues to increase with an increase in deviatoric stress under water retention, indicating that the volumetric change has experienced a compaction-expansion-compacting. The σ-ε1 curve of the sample increases first and then decreases, while the deformation in the σ2 direction shows the repeated compression and expansion. In the seepage test, the permeability–strain curve can be divided into two parts before and after fracture according to the σ-ε1 curve. Before fracture, the compression velocity of the specimen in the loading direction exceeds the expansion velocity in the unloading direction, resulting in a decrease in volume and a decrease in permeability. With an increase in deviatoric stress, fractures occur inside the particles and continue to spread from the tip until the fractures break through the shale specimen. The pore fissure area increases and the permeability of the sample increases rapidly. In terms of fracture evolution, for the water retention test, dense tensile and shear cracks appear on the failure plane perpendicular to the σ1 and σ3 directions, and complex shear fracture network appears on the failure plane perpendicular to the σ2 direction. For the seepage test, heavy shear failure occurs throughout the original fracture of the sample. With an increase in the penetration depth, the fracture shape on the failure surface perpendicular to the σ2 direction gradually changes from single to complex.