AbstractWe report the effect of substrate thickness on the optical and thermal characteristics of InGaN/GaN light emitting diodes (LEDs), operating at λ ∼ 450 nm, with different mesa sizes. For various mesa sizes with different substrate thicknesses, the junction temperature (Tj) is measured as a function of injection current by the forward voltage method and the characteristic temperature is also investigated by measuring the temperature‐dependent electroluminescence spectrum. Based on the experimentally determined heat source density, the junction temperature, heat flux, and thermal resistance (Rth) are calculated theoretically by using a three‐dimensional anisotropic heat dissipation model. The use of a thin substrate thickness of 150 µm effectively improves the heat extraction capability due to the shorter heat transfer path length. For 150 µm (443 µm) thick substrate, the Tj value of LEDs is experimentally estimated as 307.7 K (322.6 K), 311.6 K (329.5 K), and 323 K (355.9 K) under an injection current of 80 mA for 450 × 450, 400 × 400, and 300 × 300 µm2, respectively. At a high injection current of 400 mA, the Tj of 450 × 450 µm2 LED with 150 µm thick substrate is reduced by ∼25.7% compared to that of LED with 443 µm substrate thickness, indicating a value of Tj = 384.5 K. The Rth value is decreased for larger mesa size and thinner substrate thickness, resulting in Rth < 30 K/W for 450 × 450 µm2 LED with 150 µm thick substrate. The theoretically calculated Rth values indicate a good agreement with the experimentally measured data.