Southern China is susceptible to urban heat island (UHI) effect due to the rapid urbanization and subtropical climate. However, comprehensively assessing long-term UHI and its driving factors across southern China remains elusive. In this study, we investigate the UHI effect and its relationship with several critical factors in the urban agglomerations of southern China from 2003 to 2015 using remotely sensed derived products and land surface Noah model outputs. Results indicate that (1) the UHI intensity (UHII) in southern China is 1.49 K with an increasing trend of 0.011 ± 0.004 K per year. This relates to the land cover changes caused by the urbanization, which explains ∼40% of UHII trend variance; (2) Resided in the subtropical maritime climate, UHII across southern China is closely related to two climate factors: solar radiation and precipitation. Specifically, the adverse impact of precipitation on UHII is significant across southern China, where sufficient rainfall can modify soil moisture condition and improve the thermal regulation of watershed; (3) Diurnal temperature range and surface net radiation that describes surface property cannot fully explain UHII across southern China. Nevertheless, variations of sensible flux and latent flux correlate better with UHII. The sensible flux (associated with aerodynamic roughness) is responsible for 32% of UHII while the latent flux (attributed to evaporation cooling) is responsible for 13% of UHII. This result underscores the substantial contribution of sensible flux on UHI. In addition, our study suggests the effect of anthropogenic intervention may could explain the inconsistent performances of heat fluxes in responding to UHI. Our findings highlight the significance of land-atmosphere controlling factors on UHI, which have practical implications for researching urban climate.