This paper systematically reviews the mathematical modeling based on the computational fluid dynamics (CFD) method of equilibrium and nonequilibrium hypersonic flows. First, some physicochemical phenomena in hypersonic flows (e.g., vibrational energy excitation and chemical reactions) and the flow characteristics at various altitudes (e.g., thermochemical equilibrium, chemical nonequilibrium, and thermochemical nonequilibrium) are reviewed. Second, the judgment rules of whether the CFD method can be applied to hypersonic flows are summarized for accurate numerical calculations. This study focuses on the related numerical models and calculation processes of the CFD method in a thermochemical equilibrium flow and two nonequilibrium flows. For the thermochemical equilibrium flow, the governing equations, chemical composition calculation methods, and related research on the thermodynamic and transport properties of air are reviewed. For the nonequilibrium flows, the governing equations that include one-, two-, and three-temperature models are reviewed. The one-temperature model is applied to a chemical nonequilibrium flow, whereas the two- and three-temperature models are applied to a thermochemical nonequilibrium flow. The associated calculations and numerical models of the thermodynamic and transport properties, chemical reaction sources, and energy transfers between different energy modes of the three models are presented in detail. Finally, the corresponding numerical models of two special wall boundary conditions commonly used in hypersonic flows (i.e., slip boundary conditions and catalytic walls) and related research, are reviewed.