We present a formulation of a nonequilibrium Green's function method for thermal current in nanojunction atomic systems with nonlinear interactions. This first-principles approach is applied to the calculation of the thermal conductance in a one-dimensional chain and carbon nanotube junctions. It is shown that nonlinearity already becomes important at low temperatures. Nonlinear interactions greatly suppress phonon transmission at room temperature. The peak of thermal conductance is found to be around 400 K, in good agreement with experiments. High-order phonon scattering processes are important for diffusive heat transport.
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