Phonon thermal conduction was explored and discussed through a combined theoretical and simulation approach in this work. The thermal conductivity κ of polycrystalline graphene was calculated by molecular dynamics simulations based on a hexagonal patch model in close consistency with microstructural characterization in experiments. The effects of grain size, alignment, and temperature were identified with discussion on the microscopic phonon scattering mechanisms. The effective thermal conductivity was found to increase with the grain size and decrease with the mismatch angle and dislocation density at the grain boundaries (GBs). The ∼T−1 temperature dependence of κ is significantly weakened in the polycrystals. The effect of GBs in modifying thermal transport properties of graphene was characterized by their effective width and thermal conductivity as an individual phase, which was later included in a predictive effective medium model that showed degraded reduction in thermal conductivity for grains larger than a few micrometers.