It is still a challenging task to explain the uncertainty of the production of fractured geothermal reservoirs by using a parallel plate model without considering the variable aperture. Hence, we incorporated a heterogeneous aperture field with contact obstacles into a discrete fracture network (DFN) with different connection paths and densities and executed a medium-scale fluid flow and heat transfer simulation. The results show that severe flow channelization occurs in fracture systems with variable apertures, and the effective flow area is less than 40%. The increase in correlation length and contact obstacles leads to a decrease in the flow rate. The flow topology network reveals the reselection of dominant flow channels in the DFN. The effective flow intensity is independent of the fracture density and connection path length but has a negative correlation with the correlation length. The production temperature and cumulative heat energy production of the DFN model show a linear relationship with the correlation length. Finally, the strong correlation between cumulative heat production and the effective flow area emphasizes the critical role of flow channelization in the heat extraction of complex fracture systems. This study provides useful help for understanding how the micro heterogeneous aperture impacts macro production.