The anisotropic morphology of natural joints always affects their shear behavior. This experimental study aimed at exploring the anisotropic wear damage of asperities for natural joints under direct shearing tests. For casting the same joint specimens in batches, a production method for circle joint specimens containing natural joints was presented first by utilizing three-dimensional (3D) scanning and printing technologies. Then, the shear tests for natural and smooth joint specimens were carried out under different shear directions and normal stress to exhibit their anisotropic behavior. These experimental results showed that the contribution of joint asperities to shear performance (such as shear strength, dilatation deformation, and local wear damage) varied with the shear direction and exhibited anisotropic characteristics, and the anisotropy of shear strength weakened gradually with increasing normal stress due to asperity’s wear damage. For quantitatively analyzing the wear damage of a joint surface after the shear test, a technical method was also proposed to quantify the damage volume. The corresponding statistical analysis for all the experimental data indicated that the damage volume of natural joints under a shear test accumulates with increasing normal stress, but its values were different along different shear directions. The experimental study provides new clues for deciding the shearing strength parameters of natural joint for rock engineering’s design, and can also benefit the stability analysis of jointed rock mass by deeply understanding the natural joint’s strength softening and residual strength during shear failure.