The article examines the mathematical modeling of the methane tri-reforming (TRM) process based on the conservative-perturbed equilibrium (CPE) phenomenon. A comprehensive approach to modeling the TRM reactor in the COMSOL Multiphysics environment with integration of data obtained in DWSIM and MATLAB is proposed. A model of a plug flow reactor as an object with distributed parameters was obtained and studied, taking into account heat and mass transfer processes and chemical reaction kinetics on a nickel catalyst. The possibility of achieving super-equilibrium concentrations of the target product in transient CPE modes is demonstrated, which significantly increases the process efficiency. Based on the obtained temperature profiles and flow distribution analysis, a strategy for automated reactor control has been developed, aimed at maintaining optimal reaction conditions. It was established that the application of the proposed approach provides a stable temperature regime without sharp temperature drops along the reactor, which contributes to increased productivity and energy efficiency of the process. Temperature distributions of the coolant and gas mixture were obtained both along the length and in the cross-section of the reactor. This allows maintaining an optimal temperature distribution, avoiding overheating (energy efficiency) and ensuring a greater yield of the target product due to the conservative-perturbed equilibrium effect. The numerical methods such as finite difference method and finite element method, widely used for modeling heat and mass transfer processes, are implemented in various software packages, including MATLAB, ANSYS, and COMSOL Multiphysics, which allow for accurate calculations of process dynamics in reactors. The obtained results have practical significance for the automation of complex thermochemical systems with distributed parameters and optimization of their temperature regimes.