Rapid urbanisation and climate change are intensifying Urban Heat Island (UHI) effects across Southeast Asian (SEA) megacities, compounding heatwave risks and threatening urban sustainability. This study, conducted under the Asia-Pacific Network for Global Change Research (APN) collaboration, presents the first integrated, multi-decadal assessment of UHI–heatwave interactions in SEA, focusing on Kuala Lumpur as a representative pilot city. Using multi-source satellite observations, Local Climate Zone (LCZ) mapping, and the Weather Research and Forecasting (WRF) model, the research analyses both historical (2000–2024) and projected (+1°C climate perturbation) thermal dynamics. Results show persistent UHI hotspots concentrated in compact built-up LCZs (LCZ 1–3), where daytime intensity reached 4–5°C above that in vegetated areas. The mean daytime UHI was 3.6°C, while the nighttime average was 0.9°C, indicating strong diurnal contrasts linked to surface morphology. Model simulations during the April 2024 heatwave demonstrated that LCZ-informed urban canopy configurations (LCZ_local) outperformed standard schemes (RMSE ~ 2.5°C), confirming the value of localised land-use parameterisation. Under a +1°C warming scenario, UHI intensity is further amplified to 4.5°C in dense LCZs, highlighting future heat stress hotspots. Long-term heatwave analysis (1980–2024) revealed that the regional mean heatwave intensity increased by ~0.1°C², duration nearly doubled (15–30 days yr⁻¹) and frequency more than doubled (2.7–5.4 events yr⁻¹), particularly over urbanised regions such as Kuala Lumpur. This study uniquely integrates multi-decadal remote sensing, LCZ-based geospatial analysis and climate modelling to link past UHI evolution with future projections, an approach rarely undertaken in tropical developing regions. The findings provide actionable evidence for embedding LCZ-based thermal planning, green infrastructure and climate adaptation measures into SEA urban policy. The framework established here offers a replicable, science-policy pathway toward heat-resilient, low-carbon cities across the Asia-Pacific region.