High-throughput production is a major bottleneck for integration of graphene-based technologies in existing and future applications. Here, a heat transfer model is developed to optimize large-scale deposition of graphene on Ni and Cu foils in a roll-to-roll plasma chemical vapor deposition (CVD) system. Temperature distributions in Ni and Cu foils during deposition are recorded with in situ temperature measurements using near-IR optical emission spectroscopy. The model indicates that foil movement significantly affects the temperature distribution and cooling rate of the foil. Consequently, graphene growth on Cu is limited to lower web speeds for which the foil temperature is higher and the residence time in the plasma is longer. On the other hand, graphene can be deposited on Ni at relatively higher web speeds due to moderately high diffusion rate of carbon in Ni and increased cooling rates with higher web speed. Critical limitations in the production rates of graphene using roll-to-roll CVD process exist due to significant effects of web speed on the temperature distribution of the substrate. The thermal analysis approach reported here is expected to aid in enhancing the throughput of graphene production in roll-to-roll CVD systems.