We present a detailed treatment of the nonequilibrium Green's function method for thermal transport due to atomic vibrations in nanostructures. Some of the key equations, such as self-energy and conductance with nonlinear effect, are derived. A self-consistent mean-field theory is proposed. Computational procedures are discussed. The method is applied to a number of systems including one-dimensional chains, a benzene ring junction, and carbon nanotubes. Mean-field calculations of the Fermi-Pasta-Ulam model are compared with classical molecular dynamics simulations using a generalized Langevin heat bath. We find that nonlinearity suppresses thermal transport even at moderately high temperatures.