SSZ-13 membranes with high separation performances were prepared using ball-milled nanosized seeds by once hydrothermal synthesis. Separation performances of SSZ-13 membranes in CO2/CH4 and N2/CH4 mixtures were enhanced after synthesis modification. Single-gas permeances of CO2, N2 and CH4 and ideal selectivities were re-corded through SSZ-13 membranes. The effects of temperature, pressure, feed flow rate and humidity on sepa-ration performance of the membranes were discussed. Three membranes prepared after synthesis modifications had an average CO2 permeance of 1.16×10?6 mol·(m2·s·Pa)?1 (equal to 3554 GPU) with an av-erage CO2/CH4 selectivity of 213 in a 50 vol%/50 vol% CO2/CH4 mixture. It suggests that membrane synthesis has a good reproducible. The membrane also displayed a N2 permeance of 1.07×10?7 mol·(m2·s·Pa)?1 (equal to 320 GPU) with a N2/CH4 selectivity of 13 for a 50 vol%/50 vol% N2/CH4 mixture. SSZ-13 membrane displayed stable and good separation performance in the wet CO2/CH4 mixture for a long test period over 100 h at 348 K. The cur-rent SSZ-13 membranes show great potentials for the simultaneous removals of CO2 and N2 in natural gas puri-fication as a facile process suitable for industrial application.