The impact of the urban heat island (UHI) on the health of urban residents, energy consumption, as well as outdoor air quality has become increasingly significant in cities. Despite multiple recent studies on developing UHI predictive models, the impact of vertical morphological parameters on the UHI formation is barely investigated. The current work investigates the extent of vertical morphological components’ impact on the UHI intensity in urban areas and proposes a novel vertical urban morphological parameter defined as elevation index. Using remote-sensing satellite images, and a Geographical Information System (GIS) based approach, both horizontal and vertical morphological components of San-Francisco, as the case study city, were studied for 20 of its representative built up areas. High-resolution geometrical data of these areas were then correlated with the land surface temperature (LST) of those areas. Linear and nonlinear regression analysis revealed that the newly proposed elevation index has a significant impact on representing of the UHI behaviour with a coefficient of determination factor (R²) of 0.88. The model was then successfully validated against the UHI prediction of five new areas not being used for the training purposes. The impact of elevation morphology on UHI intensity was seen to be significant, especially at areas with a significant elevation variation.