Urban heat islands (UHIs) have a significantly negative impact on human health and urban sustainability. Two-dimensional (2D) landscape patterns in UHIs are well documented; however, the effects and contributions of three-dimensional (3D) urban structures remain unclear, especially across different climatic zones. We investigated the relationship between 2D/3D urban morphology and the urban thermal environment in summer and winter during the day and at night in representative large cities across four major climate zones in China. First, we extracted the seasonal surface regional heat island intensity (SRHII) using the MODIS 8-18 Day land surface temperature (LST) product. We then constructed twenty-five 2D and five 3D urban features and explored their relative importance and respective roles for UHIs in different 20 climatic contexts. Results show that: (1) there are significant differences in SRHII between various climate zones; cities with a humid subtropical climate experience temperatures around 2 °C higher during the day in summer compared to those in the other climate types. (2) 3D urban features can effectively improve the interpretation of urban features for SRHII, with an average optimization level of 21%. (3) Urban trees have a higher cooling effect than other green spaces, while taller buildings can also reduce the UHI effect. (4) On summer days, equal proportions of tree to building volume provide the greatest cooling benefit. This study provides new insights into the effect of 3D urban characteristics on SRHII and has promising implications for climate resilience planning and heat-related risk management.