The internal architecture of a CVI reactor significantly influences the gas flow behavior, as well as the complex time-varying chemical reactions, but has been typically ignored in previous CVI models. Herein we developed, validated, and applied a fully three-dimensional (3D) physicochemical CVI model of an industry-scale reactor to simulate an isothermal CVI process for fabricating bulk carbon-carbon composites using methane as a precursor gas and a multi-layered preform consisting of a non-crimp fabric and felt. The flow inside the reactor was modeled using the Navier–Stokes equation, coupled with the convection-diffusion equation, to simulate the dispersive behaviors of the reactive gases inside the porous preform. The interactive molecular diffusion of methane (CH4), ethylene (C2H4), acetylene (C2H2), and benzene (C6H6) were modeled by considering the multi-step hydrocarbon reactions between the species. The hydrocarbon concentration changes, resulting from the carbon deposition on the preform surface, were computed to predict the evolution of the preform density and porosity. The current surface area of the preform was then determined based on the current porosity. The numerical results for the average preform density agreed well with the experimental data. In addition, the present model can provide detailed simulations of the temporal and spatial evolution of the preform density that cannot be experimentally observed. The effectiveness and utility of the developed model could benefit the design of CVI reactors and processes and minimize the need for test runs when processing conditions change.