Accurate thermal properties of multiple quantum wells (MQWs) in the active region of an optically pumped vertical-external-cavity surface-emitting laser (VECSEL) are crucial for designing the thermal management of the laser. In existing related research, MQWs were regarded as bulk materials in the thermal analysis, higher thermal conductivity was employed, and the temperature rise in the active region was underestimated. We use three theoretical methods, in which various nanoscale effects are considered, to calculate the thermal conductivity of InGaAs/GaAs MQWs used in 1-μm waveband VECSEL. Theoretical results are compared to the reported experimental data, and the one more consistent with experiments is picked out. By the use of the computed thermal conductivity of InGaAs/GaAs MQWs, temperature rise in a 980-nm VECSEL is simulated and the results are in good agreement with measurements.