Shale reservoirs are the hot issue in unconventional resources. The key to the development of shale reservoirs lies in the complex fractures, which are the only path for fluid to migrate from the matrix to the wellbore in shale reservoirs. Therefore, the characteristics of shale fracture surface morphology directly affect fluid migration in shale reservoirs. However, there are few reports about the characteristics of shale fracture surface morphology as the parallel plate model was commonly used to characterize the fracture, neglecting its surface morphology characteristics and leading to great deviation. Thus, description methods were introduced to characterize shale fracture surface morphology with the aim to provide a foundation for the development of shale resources. Three shale samples were fractured by the Brazilian test, and the height distribution of the fracture surface was captured by a three-dimensional profilometer. Then, three-dimensional fracture surface morphology was regarded as a set of two-dimensional profiles, which converted three-dimensional information into two-dimensional data. Roughness, joint roughness coefficient, fractal dimension, tortuosity, and dip angle were employed to characterize shale fracture surface morphology, and their calculation methods were also, respectively, proposed. It was found that roughness, joint roughness coefficient, fractal dimension, tortuosity, and dip angle were all directional, and they varied greatly along with different directions. Roughness, joint roughness coefficient, fractal dimension, tortuosity, absolute dip angle, and overall trend dip angle were among 0.0834–0.2427 mm, 2.5715–10.9368, 2.1000–2.1364, 1.0732–1.1879, 17.7498°–24.5941°, and −3.7223°–13.3042°, respectively. Joint roughness coefficient, fractal dimension, tortuosity, and dip angle were all positively correlated with roughness.