Thermal transport in metal–organic frameworks (MOFs) is an essential but frequently overlooked property. Among the small number of existing studies on thermal transport in MOFs, even fewer have considered explicitly the influence of defects. However, defects naturally exist in MOF crystals and are known to influence many of their material properties. In this work, we investigate the influence of both randomly and symmetrically distributed defects on the thermal conductivity of the MOF UiO-66. Two types of defects were examined: missing linker and missing cluster defects. For symmetrically distributed (i.e., spatially correlated) defects, we considered three experimentally resolved defect nanodomains of UiO-66 with underlying topologies of bcu, reo, and scu. We observed that both randomly distributed missing linker and missing cluster defects typically decrease thermal conductivity, as expected. However, we found that the spatial arrangement of defects can significantly impact thermal conductivity. In particular, the spatially correlated missing linker defect nanodomain (bcu topology) displayed an intriguing anisotropy, with the thermal conductivity along a particular direction being higher than that of the defect-free UiO-66. We attribute this unusual defect-induced increase in thermal conductivity to the removal of the linkers perpendicular to the primary direction of heat transport. These perpendicular linkers act as phonon scattering sources such that removing them increases thermal conductivity in that direction. Moreover, we also observed an increase in phonon group velocity, which might also contribute to the unusual increase. Overall, we show that structural defects could be an additional lever to tune the thermal conductivity of MOFs.