The 3D digital core was reconstructed based on a CT scanning test, and the digital cores seepage simulation was investigated to study the shale's microscopic seepage characteristics. In detail, we discussed the effects of confining pressure, fluid pressure, and pore structure on the micro seepage of shale. The results showed that: (1) The confining pressure negatively affected the average velocity of the fluid, whether in pores, matrix, or the entire digital core. Due to the effect of confining pressure on fluid velocity, there was a significant negative exponential relation between permeability and confining pressure, with the confining pressure increasing from 5 MPa to 70 MPa (2) The fluid pressure positively affected the fluid velocity. Because of the effect of fluid pressure on fluid velocity, the permeability and the fluid pressure in simulation showed a significant positive exponential function relation, with the fluid pressure increasing from 1 MPa to 20 MPa (3) The fluid seepage was intensified when the flaky connected fracture was parallel to the fluid pressure direction. However, when the flaky connected fracture was perpendicular to the fluid pressure direction, it would hinder fluid seepage. (4) Permeability was positively correlated with porosity and fractal dimension but negatively correlated with tortuosity.