• Urban morphology had more influence on MRT/PET during daytime than at night. • 3D urban spatial configuration was more significantly correlated with MRT/PET than 2D pattern. • Local thermal comfort was mainly impacted by BFAR during daytime and by TCCR at night. • Evaluating effects of urban morphology on local thermal comfort should control the effects of BFAR. Urban morphology has significant effects on local thermal comfort. To investigate the correlation between thermal condition and urban spatial configuration, 24 typical scenarios were extracted from complex urban area, and 17 2D/3D indicators were selected to represent urban morphology characteristics. Different statistical approaches were employed to quantify the relationship between the selected indicators and MRT/PET. The results showed: (1) urban morphology exerted more influences on local thermal condition during daytime than at night, leading to the spatial heterogeneity of MRT/PET being much higher in the daytime; (2) the correlations between urban morphology indicators and MRT/PET changed dramatically when using different statistical approaches. This finding highlights the necessity of controlling the effect of building floor area ratio when quantifying the impacts of urban spatial configuration on local thermal comfort; (3) 3D urban morphology indicators were more significantly correlated with local thermal comfort than 2D indicators. Specifically, building floor area ratio and tree canopy coverage ratio were the most important predictor of MRT/PET during daytime and at night respectively. This study could further strengthen our understanding the effects of urban morphology on UHI. It could also offer useful insights to urban planners and decision makers on designing and constructing climate-adaptive urban environment.