Enhancing the efficiency of hydraulic fracturing is crucial in developing unconventional reservoirs, where fracture roughness commonly arises and strongly affects proppant transport behavior. However, it often results in rough fractures that accompany various problems. Addressing these issues, a validated computational fluid dynamics-discrete element method (CFD-DEM) approach was employed, and a narrow rough fracture model was developed using the spectral synthesis method to investigate proppant transport during hydraulic fracturing. Initially, the model was validated against previous research, followed by examining the relationship between changing flow regimes and force characteristics compared to continuous fractures. The impact of injection velocity, fracture inclination angle, and fluid viscosity on flow regimes and micro-internal mechanisms was also analyzed. The findings reveal distinct flow regimes and force characteristics of blocky dunes compared to continuous dunes. Notably, the drag force curve exhibits two stages in the proppant transport process: the settlement-dominant and scour-dominant stages. Furthermore, the results indicate two micro-mechanisms for improving proppant transport efficiency: reducing particle–particle interaction forces and prolonging particle settling time, the latter of which can be effectively achieved by increasing fluid viscosity. Finally, a multi-factor analysis based on an orthogonal test method is conducted to evaluate the combined influence of key parameters. This study significantly advances our understanding of proppant transport in rough fractures and offers valuable insights for optimizing injection parameters.