The local heat transfer coefficient (LHTC) can be an effective indicator to describe the local heat transfer characteristics of fractures but has rarely been employed to investigate the local heat exchange properties of a hot dry rock fracture compared to the overall heat transfer coefficient (OHTC). The aim of this paper is to investigate the LHTC of water flowing through a single fracture within a cylindrical granite specimen under confining pressure by combining the numerical modeling approach and the experimental results. A numerical model was successfully developed and verified by the test data. It is found that the local heat transfer coefficient is obviously closely related to the fluctuation of the fracture morphology. Within a certain range of aperture, narrower fracture has higher local heat transfer ability. Increasing the flow rate did not significantly improve the local heat transfer ability in the flat area of the fracture for a fixed fracture aperture. However, at the rougher areas, the flow rate has a higher effect, and the sunken positions at the fracture surface have much larger LHTC. A correlated model was developed to describe the relationship between waviness and LHTC. In addition, a comparison between the LHTCs and the OHTCs shows that the definition-based method presents the smallest values of the OHTCs, which are the closest to the arithmetic mean values of the corresponding LHTCs.