Demands for engineering thermal transport properties are ever increasing for a wide range of modern micro- and nanodevices and materials-based energy technologies. In particular, there is a severe situation due to the rapid progress in the synthesis and processing of materials and devices with structural characteristic length on the nanometer scales, which are comparable or even smaller than the intrinsic length scales (such as mean free path and wavelength) of basic energy carriers (such as phonons, electrons, and photons). Although advanced approaches for controlling the electronic and photonic transport have been proposed in the past decades, progress on controlling lattice vibrations (i.e., the phonons) is still far behind. Gaps between the fundamental understandings of the behavior of the basic energy carriers at small scales and the technological demands still remain, particularly from a computer modeling point of view. Herewith, we give a perspective of the computational approaches for predicting the thermal transport properties of low-dimensional materials and nanostructures, which are mainly sorted into three categories: empirical molecular dynamics, anharmonic lattice dynamics based Boltzmann transport equation, and Landauer theory. The advantage and disadvantage of each method are discussed and some possible solutions are suggested. The discussion is focused on fully and accurately characterizing the mode-level phonon behavior, possible all-order phonon scattering process, and incorporation of realistic nanostructures. Moreover, emerging challenges of phonon coupling effects, such as electron-phonon, phonon-photon, and phonon-magnon coupling, are also discussed. We expect that this perspective will stimulate future research in computer modeling of micro-/nanoscale heat transfer beyond traditional phonons.