The ideal development of layer-bound, polygonal faults occurs in an isotropic stress field. However, some populations of layer-bound faults appear to have originated as ‘polygonal’ faults, but display atypical plan-view fault geometries that suggest development under anisotropic stress conditions. High-resolution 2D/3D seismic data in the southern Qiongdongnan Basin displays three tiers of layer-bound faults with distinct strike variations and complex structural patterns that depart from the geometries of isotropic polygonal fault cells. The lower fault tier displays preferred orientations along E-W, NE-SW, NW-SE directions; the middle fault tier shows a primary E-W orientation and a secondary N-S trend; the shallow tier features strong N-S and E-W orientations. Fault patterns in map view include orthogonal, quasi-polygonal and circumferential geometries, among which the orthogonal pattern is dominant in the shallow fault tier. Several factors are inferred to cause these variable geometrical and structural patterns in layer-bound faults, they are: pre-existing tectonic faults, an uplifted region, local slopes, contourite depressions, and large contourite-related channels. The orthogonal fault patterns have longer E-W orientation parallel to the contourite channels and shorter N-S trends perpendicular to the thalwegs. The presence of submarine channels is suggested to locally deflect the stress orientation, which in turn impacts fault patterns.