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Quantifying vegetation fractional cover (VFC) and assessing its role in heat fluxes modeling using medium resolution remotely sensed data has received less attention than it deserves in heterogeneous urban regions. This study examined two approaches (Normalized Difference Vegetation Index (NDVI)-derived and Multiple Endmember Spectral Mixture Analysis (MESMA)-derived methods) that are commonly used to map VFC based on Landsat imagery, in modeling surface heat fluxes in urban landscape. For this purpose, two different heat flux models, Two-source energy balance (TSEB) model and Pixel Component Arranging and Comparing Algorithm (PCACA) model, were adopted for model evaluation and analysis. A comparative analysis of the NDVI-derived and MESMA-derived VFCs showed that the latter achieved more accurate estimates in complex urban regions. When the two sources of VFCs were used as inputs to both TSEB and PCACA models, MESMA-derived urban VFC produced more accurate urban heat fluxes (Bowen ratio and latent heat flux) relative to NDVI-derived urban VFC. Moreover, our study demonstrated that Landsat imagery-retrieved VFC exhibited greater uncertainty in obtaining urban heat fluxes for the TSEB model than for the PCACA model.