Abstract The thermal conductivity of defected graphene nanoribbons(GNRs) was studied using equilibrium molecular dynamics simulation. It was demonstrated that the thermal conductivity of GNRs is extremely sensitive to defect configuration. The enhanced scattering at the boundaries will reduce thermal conductivity, the narrower the ribbon is, the stronger the boundary effect is. Hydrogen passivation is exploited to weaken the boundary effect, new scattering mechanisms, however, appears due to sp2-to-sp3 transformation as well as mass difference between hydrogen and carbon. Moreover, Stone–Wales (SW) defects may increase the scattering of phonons and thus reduce thermal conductivity, especially in the case with SW defect arrays perpendicular to the direction of heat flow. Therefore, the defects should be avoided in the fabrication of graphene for good thermal conductivity.