Hot dry rock (HDR) is deep geothermal reservoir rock predominantly containing granite, whose physical and mechanical properties are governed by heterogeneous crystal structures. However, the fluid conductivity of intact granite with ultra-low permeability cannot be reformed using existing techniques. Complex fracture networks must be created by connecting hydraulic fractures with natural fractures developed in reservoirs. In this study, we introduce the wall barrier method into the novel hydro-grain-based model (hydro-GBM) to build a prefractured granite model at the mineral grain scale. This model enables investigation of the effects of the stress environment, mineral spatial distribution, and fluid injection rate on hydraulic fracturing characteristics. Microcracks around the inner tips of pre-existing fractures reproduce the initiation, propagation, and coalescence behaviors similar to experimental results. Mineral spatial distributions induce random changes in the propagation paths of hydraulic fractures. Increasing the fluid injection rate delays the deflection of hydraulic fractures and extends the propagation distance along the major axes of pre-existing fractures. The average activity level and proportion of large seismic events are reduced by injecting low-rate fluid. In summary, our results reveal the interactions between hydraulic and pre-existing fractures and provide a valuable reference for constructing an efficient enhanced geothermal system (EGS) for deep reservoirs.