Optimizing the quantum structures in the active region and improving the thermal management are crucial for upgrading the output power of an external-cavity surface-emitting laser. The above two methods are all based on the accurate thermal analysis of the laser, and depended on a key material parameter, the thermal conductivity. Because the multiple quantum wells and the distributed Bragg reflector in an external-cavity surface-emitting laser are typical nanostructures, properties of nanoscale thermal conduction are considered, and three analytical methods are used to calculate thermal conductivities of GaAs/AlAs distributed Bragg reflectors with different thicknesses. Theoretical results are compared with reported experiments and the method which is more proper to compute the thermal conductivity of GaAs/AlAs system nanostructure is selected. By use of the selected analytical method, thermal conductivities of InGaAs/GaAs multiple quantum wells and GaAs/AlAs distributed Bragg reflector in a 980 nm external-cavity surface-emitting laser are simulated. It is found that the cross-plane thermal conductivity of distributed Bragg reflector is about 40% of the value of corresponding bulk material, while the cross-plane thermal conductivity of multiple quantum wells is less than half of the bulk material. Numerical analysis of the temperature rise in the gain chip is carried out using the obtained thermal conductivities, and the results are in good agreement with experiments.