The challenges in developing high CO2 gas fields are governed by several factors such as reservoir condition, feed gas composition, operational pressure and temperature, and selection of appropriate technologies for bulk CO2 separation. Thus, in this work, we report an optimization study on the separation of CO2 from CH4 at high CO2 feed concentration over a functionalized mixed matrix membrane using a statistical tool, response surface methodology (RSM) statistical coupled with central composite design (CCD). The functionalized mixed matrix membrane containing NH2-MIL-125 (Ti) and 6FDA-durene, fabricated in our previous study, was used to perform the separation performance under three operational parameters, namely, feed pressure, temperature, and CO2 feed concentration, ranging from 3.5–12.5 bar, 30.0–50.0 °C and 15–70 mol%, respectively. The CO2 permeability and CO2/CH4 separation factor obtained from the experimental work were varied from 293.2–794.4 Barrer and 5.3–13.0, respectively. In addition, the optimum operational parameters were found at a feed pressure of 12.5 bar, a temperature of 34.7 °C, and a CO2 feed concentration of 70 mol%, which yielded the highest CO2 permeability of 609.3 Barrer and a CO2/CH4 separation factor of 11.6. The average errors between the experimental data and data predicted by the model for CO2 permeability and CO2/CH4 separation factor were 5.1% and 3.3%, respectively, confirming the validity of the proposed model. Overall, the findings of this work provide insights into the future utilization of NH2-MIL-125 (Ti)/6FDA-based mixed matrix membranes in real natural gas purification applications.