The interaction between urban heat island (UHI) and heatwaves (HWs) shapes urban extreme heat, but whether HW-induced UHI amplification reorganises canopy-to-boundary-layer thermal structure, and whether local climate zones (LCZs) modulate this response, remains unclear. Here, we investigated two July 2020 HW events in the Guangzhou metropolitan area in southern China, using 1 km LCZ-coupled Weather Research and Forecasting (WRF) simulations. We analysed the vertical thermal response of the urban area and individual LCZs using canopy and boundary-layer UHI intensities (CUHII, BUHII), layer-mean urban–rural air-temperature differences (Layer ∆T ), and surface-energy-balance and turbulence indicators. HWs amplified both CUHII and BUHII in a vertically non-uniform manner: CUHII increased more than BUHII, and additional warming concentrated in the canopy and lower boundary layer. Warming propagated upward as the daytime boundary layer developed but contracted toward the surface at night and during transition periods, with upper-level responses weakening or reversing. LCZ heterogeneity was largely confined to the lowest ∼250 m: LCZ 1 showed the strongest additional warming, LCZ 2 and LCZ 4 reached comparable levels through different energy–turbulence pathways, and LCZ 6 was weakest. Stronger sensible heat flux, higher Bowen ratios, sustained nocturnal heat sources, and reduced low-level stability jointly drove this diurnal reorganisation. During HW1, residual-layer warm anomalies in LCZ 1 ( 0.41 °C at 500–600 m) persisted through the night and provided an additional heat reservoir for next-day mixed-layer development, whereas LCZ 6 showed much weaker memory effects. HW2 reproduced the inter-LCZ ranking with weaker absolute amplitude.