Seismic anisotropy originating within the continental crust is commonly used to determine the deformation and kinematic flow within active orogens and is attributed to regionally oriented mica or hornblende grains. However, naturally deformed rocks usually contain compositional layers (e.g., parallel compositional banding). It is necessary to understand how both varying mineral contents and differing intensities of compositional layering influence the seismic properties of the deep crust. In this study, we analyzed the seismic response of migmatitic amphibolite with compositional banding structures. We present the microstructures, fabrics, calculated seismic velocities, and seismic anisotropies of mylonitic amphibolite from a horizontal shear layer preserved within the Ailao Shan-Red River shear zone, southwestern Yunnan, China. The investigated sample is characterized by pronounced centimeter-scale compositional banding. The microstructures and fabrics suggest that migmatitic amphibolite rocks within deep crust may delineate regions of deformation-assisted, channelized, reactive, porous melt flow. The origin of compositional banding in the studied migmatitic amphibolite is attributed primarily to partial melting together with some horizontal shearing deformation. The microfabrics and structures investigated in this study are considered to be typical for the base of active horizontal shear layers in the deep crust of southeastern Tibet. Seismic responses are modeled by using crystal preferred orientations for minerals of the migmatitic amphibolite by applying the Voigt-Reuss-Hill homogenization method. Calculated P-wave and S-wave velocities are largely consistent in the various layers of the migmatite. However, seismic anisotropies of P-wave (AVp) and S-wave (AVs) are higher in the melanosomes (AVp = 5.6%, AVs = 6.83%) than those in the leucosomes and the whole rock (AVp = 4.2%–4.6%, AVs = 3.1%–3.2%). In addition, there is pronounced, S-wave splitting oblique to the foliation plane in the migmatitic amphibolite. The multiple parallel compositional layers generate marked variation in the geometry of the seismic anisotropy (Vs1 polarization) in the whole rock. Combined with the macroscale geographical orientation of fabrics in the Ailao Shan-Red River shear zone, these compositional banding effects are inferred to generate significant variations in the magnitude and orientation of seismic anisotropy, especially for shear-wave anisotropy (AVs) in the deep crust. Hence, our data suggest that layering of various origins (e.g., shear layers, partial-melting layers, and compositional layers) represents a new potential source of anisotropy within the deep crust.