The poor thermal design of high brightness light-emitting diodes (HB-LEDs) package for the automotive exterior lighting system causes the degradation of the optical and reliability performance, also the deterioration of the costeffectiveness. We design the flexible package substrate with the thick heat-spreading layer and thermal via-hole fully filled with the copper (FFC) for the conventional process of flexible printed circuit board (FPCB) and the extraction methodology of the heat flow is presented. Effective heat flow for thermal simulation is compensated for the optical loss between the internal and external quantum efficiency. The vertical blue LED is attached on metal core printed circuit board (MCPCB) without the molding process, and then heat distribution and optical power is, respectively, measured by using infrared camera and optical LED tester as increasing the magnitude of the input power. Detailed thermal performance of FPCB and MCPCB is verified with the heat distribution and the thermal resistance. The effects of the main factors of FPCB with filled via-holes are discussed using design of experiment (DOE) methodology. The thermal resistance and junction temperature of FPCB is, respectively, over two times and 10 ℃ lower than that of MCPCB.