AbstractGeothermal energy is sustainable and gaining momentum as a solution to energy crises and environmental issues. However, challenges like production temperature and thermal breakthrough can impact geothermal project efficiency. One innovative solution to alleviate the thermal breakthrough is to inject polymer‐based materials that are encapsulated in microcapsules into fractures to modify fracture permeability and prevent preferential flow. In our study, we utilized a coupled computational fluid dynamics and discrete element method to simulate the transport of microcapsules under various scenarios controlled by microcapsule size, microcapsule concentration, and fracture roughness. For a smooth fracture, the results indicate that small microcapsules can travel through a smooth fracture regardless of their concentrations. Large microcapsules can transport through a smooth fracture when present in lower concentrations. However, medium and mixed‐size microcapsules tend to cause the sealing of a smooth fracture, irrespective of their concentrations. For a rough fracture, the transport of microcapsules is complicated by their interactions with the rough fracture walls. The presence of two sealing positions in a rough fracture adds further complexity to this transport phenomenon. The size and concentration of microcapsules control one sealing location, while the rough fracture walls determine the other sealing location. The rough walls substantially affect microcapsule transport, rendering the role of microcapsule size and concentration less significant. The simulation results suggest that complex fracture surfaces significantly elevate the occurrence of sealing behavior. To mitigate sealing behavior within more complex fractures, it would be beneficial to use smaller and lower concentrations of microcapsules.