This paper aims at developing a thermal atlas system at the urban district scale to evaluate the urban thermal environment and identify thermally vulnerable areas. Shanghai Lujiazui Central Business District was selected as a test bed for the method. Six key morphological indicators, i.e., sky view factor, pavement cover ratio, vehicle traffic density, green plot ratio, frontal area index and proximity to heat sink were used to describe different aspects of the urban thermal environment including building density, land use, anthropogenic heat, greenery, ventilation potential and heat sink. Spatial analysis tools were developed in geographical information system to generate maps for these morphological indicators. In situ meteorological measurements were carried out on peak summer days to investigate the spatial variation of microclimatic parameters, based on which the physiological equivalent temperature (PET) index was calculated. Empirical regression models were built correlating PET values with local morphological indicators, based on which PET maps were generated. This thermal atlas system can rapidly analyze and visualize the spatial variations of urban microclimate from the thermal comfort aspects as affected by different urban design scenarios, thus can be a useful decision-support tool for urban design towards alleviating urban heat island intensity and improving outdoor thermal comfort. (C) 2015 Elsevier B.V. All rights reserved.