InGaAs/InGaAsP quantum well structures have wide applications, such as the integration of optoelectronic devices and low threshold current density laser, as well as low loss waveguides and optical switching elements. In many case, high temperature operations are necessary during the course of processing a wafer. Here, we report the influence of low and high etch pit densities (EPD) InP substrates on the thermal stability of InGaAs/InGaAsP quantum well laser structure. Both the n-type of S-doped (EPD<500 cm-2)and Sn-doped (EPD≈5x104cm-2) InP substrates were grown under the same run with half wafer each. To assess the thermal stability, the samples were annealed, using a rapid thermal processor, between 650 °C and 750 °C, for 60 seconds. 77 K photoluminescence measurements were performed on the samples after annealing to study the degree of bandgap shift. It was found that S-doped InP substrate with low EPD, i.e. low point defect density, is thermally stable up to an annealing temperature of 625 °C for 60 seconds. Compared to the S-doped materials, laser structure grown on the Sn-doped InP substrate was found to exhibit larger degree of bandgap shift resulted from defects induced quantum well intermixing.