Production simulation from fractured shale reservoirs is often performed by simplifying the hydraulic fractures as rectangular planes with homogeneous aperture. This study investigates the effects of heterogeneous fracture aperture and proppant distribution in realistic, non-rectangular fractures on the multi-phase production from shales. The heterogeneous hydraulic fractures are generated with the GEOS multiphysics simulator under realistic 3D stress field. These fractures are embedded into the TOUGH+ multi-phase flow simulator for production simulation. The results emphasize the importance of flow barriers within the hydraulic fractures, due both to low-aperture regions caused by the stress-shadow effect and the settling of proppant. The production rate is particularly sensitive to aperture heterogeneity if the flow barriers are close to the wellbore such that a great portion of fracture volume is isolated from the well. A stage-to-stage comparison reveals that production from different stages could vary significantly because the local stress field leads to different fracture area and aperture. The use of proppant prevents fracture closure, but if the propped regions are far from the well, they do not enhance production because flow barriers between these regions and the well act as bottlenecks. The present study highlights the importance of incorporating aperture heterogeneity into production simulation, provides insights on the relationship between flow barriers, proppant concentration, and well production, and proposes a practical method to mitigate numerical difficulties when modeling heterogeneous fractures.