This whitepaper details a systematic methodology for concurrent development of reactor-scale physical model and model-based process control development for metal-organic chemical vapor deposition (MOCVD). The example used for illustrating the approach is the deposition of yttrium-barium-copper oxide (YBa2Cu3O7-x or YBCO) thin films with high temperature superconducting (HTS) properties. Information about the gas-phase chemical mechanisms, obtained from experimental data in the literature, is used in the reactor-scale transport and kinetics model developed using the CFD-ACE™ software package. These models were used to design model-based controllers for desired deposition rate, and for uniformity of deposition rate and stoichiometry within wafer. These simulation tools and the results obtained from the studies provide a clearer understanding of the chemical mechanism, species transport, and film growth. This understanding enables design and implementation of optimized controllers that meet both process specifications as well as run-to-run repeatability, which are essential for large-scale production.