Rarefied gas flows through two-dimensional micro channels are studied numerically for the performance optimization of a nanomembrane-based Knudsen compressor. The effects of the wall temperature distributions on the thermal transpiration flow patterns are examined. The flow has a pumping effect, and the mass flow rates through the channel are calculated. The results show that a steady one-way flow is induced for a wide range of the Knudsen number. The DSMC(direct simulation Monte Carlo) method with VHS(variable hard sphere) model and NTC(no time counter) techniques has been applied in this work to obtain numerical solutions. A critical element that drives Knudsen compressor Is the thermal transpiration membrane. The membranes are based on aerosol or machined aerogel. The aerogel is modeled as a single micro flow channel.