The coherent quantum effect becomes increasingly important in the heat dissipation bottleneck of semiconductor nanoelectronics with the characteristic size shrinking down to few nano-meters scale nowadays. However, the quantum mechanical model remains elusive for anharmonic phonon-phonon scattering in extremely small nanostructures with broken translational symmetry. It is a long-term challenging task to correctly simulate quantum heat transport including anharmonic scattering at a scale relevant to practical applications. In this article, we present a clarified theoretical formulation of anharmonic phonon non-equilibrium Green function (NEGF) formalism for both 1D and 3D nanostructures, through a diagrammatic perturbation expansion and an introduction of Fourier representation to both harmonic and anharmonic terms. A parallelized computational framework with first-principle force constants input is developed for large-scale quantum heat transport simulation. Some crucial approximations in numerical implementation are investigated to ensure the balance between numerical accuracy and efficiency. A quantitative validation is demonstrated for the anharmonic phonon NEGF formalism and computational framework by modeling cross-plane heat transport through silicon thin film. The phonon-phonon scattering is shown to be appreciable and to introduce about 20% reduction of thermal conductivity at room temperature even for a film thickness around 10 nm. The present methodology provides a robust platform for the device quantum thermal modeling, as well as the study on the transition from coherent to incoherent heat transport in nano-phononic crystals. This work thus paves the way to understand and to manipulate heat conduction via the wave nature of phonons.