A steady-state three-phase heterogeneous model was applied for simulation of a vacuum gas oil (VGO) hydrotreating reactor in both pilot and industrial plants under non-isothermal conditions. Three main reactions, including hydrodesulfurization (HDS), hydrodearomatization (HDA), and hydrodenitrogenation (HDN), were considered, and various kinetic models were evaluated to justify the commercial reactor predictions. The influence of important operating variables, such as feed American Petroleum Institute (API) gravity, temperature, pressure, and liquid hourly space velocity (LHSV), were studied. Evaluation of simulated results showed that component concentration profiles are very close in liquid and solid phase and the model can be renewed to a pseudo-two-phase model. Thus, the differential-algebraic equations (DAEs) were converted to particularly stiff ordinary differential equations (ODEs) and solved simultaneously with the Simulink toolbox in MATLAB. The simulation was validated by pilot- and industrial-plant hydrotreater data with good agreement. With the implementation of the hydrotreater simulation in the Simulink well, the dynamic behavior studies are simplier and easier for any commercial hydrotreating reactor.