This study employs an evaluated Surface Urban Energy and Water Balance Scheme (SUEWS) model driven by Local Climate Zone (LCZ)-derived urban canopy parameters to explore landscape heterogeneity's impacts on the partitioning of surface energy fluxes and heat stress variations in Lagos, Nigeria. The results reveal that LCZ-based SUEWS effectively replicates the diurnal patterns of air temperature (Tair), relative humidity (RH), and land surface temperature (LST). The root mean square error (RMSE) for simulated Tair and RH ranges from 0.4 °C to 1.2 °C and 1.8% to 8.0%, respectively. While a nighttime warm bias in LST is observed, it reduces during the daytime. Significant spatial variability in turbulent heat fluxes and LST among LCZs is noted, with core urban LCZs experiencing notable increases in sensible heat flux and LST, while suburban LCZs exhibit higher latent heat flux values. Anthropogenic heat flux peaks in high compact low-rise LCZ 3, reaching a maximum of 95 W/m2. Remarkably, no significant difference is found in the diurnal heat stress cycle among LCZs, despite consistently elevated heat stress levels in high compact LCZs. These findings offer valuable insights into quantifying surface energy flux variabilities and spatio-temporal heat stress patterns in a densely populated tropical city- Lagos Nigeria. •SUEWS simulated high-res weather variables in a tropical high-dense city.•Urban land cover significantly affects surface energy fluxes.•Compact, dense LCZs exhibit higher turbulent heat fluxes and LST.•Anthropogenic heat flux estimated at 23 W/m2, with peaks up to 95 W/m2.