Manipulating thermal conductivity through nanoengineering is of critical importance to advance technologies, such as soft robotics, artificial skin, wearable electronics, batteries, thermal insulation, and thermoelectrics. Here, by examining amorphous polymers, including polystyrene, polypropylene, polyethylene, and ethylene vinyl alcohol, using molecular dynamics simulations, we find that the thermal conductivities of amorphous polymers can be reduced below their amorphous limit by size effects. Size-dependent thermal transport in amorphous materials is decomposed into crystalline, crystalline-to-amorphous, and amorphous regimes. In the amorphous regime, the mean free path of propagating heat carriers can range from tens of nanometers to more than 100 nm, contributing 16%–36% of the total thermal conductivity. A two-channel model that combines no size effect (i.e., difusons and locons) and size effect (i.e., propagons) is proposed to account for size-dependent thermal conductivity. We also find that the presence of charged molecules in polymers can significantly affect the thermal conductivity and its size effects due to electrostatic interactions. This work provides insights into the thermal conductivity of amorphous polymers that will have a broad impact on the nano- and chemical engineering of polymers for various energy-related applications.