The present study deals with the synthesis of nanostructured silicalite-1 membranes on porous α-Al₂O₃ supports by a hydrothermal method. Different parameters including the synthesis conditions (temperature and alkalinity) and operating conditions (temperature and pressure) were investigated. The membranes were characterized by X-ray diffraction and scanning electron microscopy techniques. The optimum synthesis temperature and alkalinity were determined to be 160 °C and pH = 11, respectively. The permeability of CO₂ and CH₄ through the optimized membrane was determined by the pressure drop method. The results revealed that the main effective separation mechanism was adsorption. The permeation of CO₂ and CH₄ declined with increasing temperature, whereas high feed pressures enhanced the single gas flux. The CO₂ and CH₄ permeability values at 30 °C and 2 bar were 1.62 × 10⁻⁷ and 2.07 × 10⁻⁷ mol m⁻² s⁻¹ Pa⁻¹, respectively. Furthermore, the response surface methodology analysis confirmed the significance of all the variables and the proposed model. Excellent correlation between the experimental and predicted data (R² = 0.99) was obtained, confirming that response surface methodology is a powerful tool for modeling nanostructured silicalite-1 membrane processes.