Geothermal 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. Geothermal energy is a sustainable solution to energy and environmental challenges, but it faces efficiency issues due to factors like production temperature and thermal breakthrough. A novel solution involves injecting polymer-based microcapsules into fractures to modify permeability and prevent preferential flow. Our study used numerical simulations to explore how different factors, such as microcapsule size, microcapsule concentration, and rough fracture, affect microcapsule transport. In a smooth fracture, small microcapsules can travel easily, while large microcapsules transport at lower concentrations. However, middle and mixed-size microcapsules tend to seal a smooth fracture. A rough fracture complicates the transport, with sealing positions influenced by microcapsule size, concentration, and interactions with rough walls. It is favorable to use smaller microcapsules at lower concentrations for complex fractures to mitigate sealing behavior. Middle and mixed-size microcapsules have a higher propensity for sealing a smooth fracture compared to small or large microcapsules In the case of a rough fracture, the presence of rough fracture walls substantially increases the likelihood of sealing the fracture In certain rough fracture cases, two sealing locations can be observed