The purification of raw natural gas is critical for removing contaminants such as water vapor, gas condensates, and mechanical impurities that can impair downstream equipment and reduce gas quality. In this study, we present a comprehensive modeling, simulation, and experimental analysis of a modified three-phase gas-liquid separator tailored for high-load natural gas streams. The separator design incorporates thirty suspended baffles and a novel anti-foam mesh, which were geometrically optimized using experimental fluid dynamics principles. Aspen Plus simulations were performed using the Peng-Robinson thermodynamic model with a detailed three-phase flash separation module. Feed composition from the Somontepa gas field was used (CH₄: 89.65%; CO₂: 4.12%; H₂S: 3.00%; C₂–C₆+: 2.55%), at 5.6 MPa and 25°C. The simulation accurately predicted the phase split, showing that 98.3% of the hydrocarbon vapor was directed to the gas outlet, while >99% of condensates and water were captured in the liquid phase. Sensitivity analysis across 20–65 m/s inlet velocities revealed that the pressure drop was reduced by 27% in the enhanced baffle configuration. Furthermore, Aspen Plus predicted a 96.8% decrease in entrained liquid carryover compared to a baseline separator. The results were validated through field trials, which confirmed the simulation predictions: gas condensate content was reduced from 16.58 to 0.725 g/m³, moisture from 4.84 to 0.1 g/m³, and mechanical impurities from 1.2 to 0.0058 g/m³. This synergy of simulation and practice highlights the robustness of the improved design for deep natural gas decontamination and positions it as a scalable solution for industrial gas processing plants.