Self-propping fractures formed during hydraulic fracturing in shale reservoirs constitute a critical component of the hydraulic fractures, with surface roughness serving as a pivotal factor governing their mechanical and hydraulic properties. To examine the regulatory effects and underlying mechanisms of rough morphology on fluid transport behavior within self-propping fractures under closure stress, this study employs the fast Fourier transform (FFT) method to generate synthetic rough fractures characterized by fractal Brownian motion (FBM) features. Subsequently, a coupled mechanical-hydraulic model for single rough self-propping fractures was established to simulate the influence of morphological roughness on their hydrodynamics characteristics. The results demonstrate that under closure stress, the deformation increment of self-propping fractures exhibits a pronounced synchronous relationship with fracture conductivity degradation. The progressive narrowing of fracture aperture induced by increasing closure stress constitutes the primary mechanism driving persistent conductivity deterioration. Furthermore, both high-density “cluster-like” contact micro-asperities and “throat-shaped” constriction structures have been identified as critical morphological factors. Regions dominated by the high-density “cluster-like” contact micro-asperities significantly constrict the flow pathways, inducing specialized flow phenomena such as “transverse flow” and “reverse flow”. Concurrently, the “throat-shaped” constriction structures generate significant throttling effects, precipitating abrupt pressure drops. These combined mechanisms fundamentally degrade the conductivity of self-propping fractures under closure stress. A linear positive correlation exists between fractal dimension and fracture conductivity. While closure stress induces significant reconfiguration of flow pathways, the interplay between fractal roughness characteristics and stress-induced deformation preserves the integrity of favorable flow conduits, resulting in higher conductivity with larger fractal dimensions. Fracture conductivity is governed by the competitive interaction between the roughness-mediated reduction in flow resistance and the throat constriction effect during mechanical compression. The primary flow pathways within self-propping fractures are predominantly dictated by the fundamental large-scale morphological structures. In contrast, small-scale roughness features primarily enhance flow heterogeneity in velocity magnitude and direction. Crucially, these secondary structures do not fundamentally alter the spatial distribution pattern of the primary flow channels in self-propping fractures.