As a new type of unconventional natural gas resource, shale gas plays a vital role in energy supply. In order to deeply understand the shale fracture seepage characteristics, filled and unfilled fracture seepage tests were carried out on shale samples with different fracture surface topography with the use of self-developed shale fracture seepage testing equipment. The fitting formula that the seepage discharge decreased as a negative exponential function with the increase in normal stress was obtained in the unfilled fracture seepage test; the fitting coefficient had a good logarithmic and exponential function relationship with joint roughness coefficient JRC and surface development interface area ratio Sdr. Meanwhile, the modified cubic law was obtained by adding the correction coefficient. The correction coefficient had an exponential relationship with the anisotropy value Ka. Compared with the unfilled one, the fracture surface topography had little effect on the seepage discharge when it was filled. The experimental results show the effects of water head difference, fracture surface topography, particle size, and thickness of filling sand on shale fracture seepage characteristics under different normal stress conditions, which have a certain significance for improving the efficiency of shale gas production.