The hybrid fixed-site-carrier (FSC) membranes were prepared by coating the carbon nanotubes (CNTs) reinforced polyvinylamine (PVAm)/polyvinylalcohol (PVA) blend selective layer on the top of the polysulfone (PSf) ultrafiltration membranes. The influences of membrane preparation parameters of support, heat treatment condition and pH value of casting solution on the membrane separation performance were systematically investigated. The hybrid FSC membranes prepared under the optimal condition (PSf 20 K − 95 °C − 0.75 h – pH 10) showed high CO2 permeance and relatively good CO2/CH4 selectivity based on high pressure gas permeation testing. Moreover, process operating parameters such as feed pressure, temperature, feed CO2 concentration, and feed flow rate as well as water vapor content were found to significantly affect the membrane performance, which need to be optimized in the real application. Small pilot-scale modules with relatively large membrane areas (110–330 cm2) were additionally tested. The results could be used to guide process simulation and economic feasibility analysis of CO2 removal from high pressure natural gas process with the developed FSC membranes in the future work.