Understanding the urban thermal environment is vital for improving urban planning and strategy development when mitigating urban heat islands. However, urban thermal characteristics of local climate zones (LCZ) are different within cities and most studies lack regional perspective. This study explored surface thermal performances of cities in three urban agglomerations (Jing-Jin-Ji, Yangtze River Delta and Pearl River Delta) in China using MODIS land surface temperature (LST). Besides that, the diurnal and seasonal LST variations of LCZs are also studied. Moreover, the optimal LCZs for better urban cooling are also investigated in this study. Although the thermal distributions of LCZs are different in China, there are still some similar features. Our four key findings were as follows. (1) LCZs in China are well classified, with average overall accuracy of 82% being higher than that in some previous studies. (2) The LST of mid-rise (LCZ 2, 5) is higher than that of high- and low-rise buildings (LCZ 1, 3, 4, 6); and compact buildings are warmer than open buildings (LCZ 1–3 > LST 4–6) in summer of China. That shows both mid-rise and compact buildings are not beneficial to cool urban. In addition, LST variations at daytime and in summer are more significant than nighttime and other seasons. (3) LST differences within LCZs are significant at p < 0.05, and are most significant in Jing-Jin-Ji (JJJ). The LST difference within built types (LCZ 1–10) is more significant than within natural types (LCZ A–G), showing that built types alteration will be more effective for thermal environmental improvement. (4) Under the current population and urban area, increasing greenness and water area in compact high-rise buildings are the most effective strategies for urban cooling in all three urban agglomerations, with the largest reduction in LST of 4.11 K in JJJ. These findings will provide support for thermal environment mitigation, urban planning and sustainable urban development.