Micro-electromechanical systems and nano-electromechanical systems have attracted a great deal of attention in recent years. The flow and heat transfer behaviors of micromachines for separation applications are usually different from that of macro counterparts. In this paper, heat and mass transfer characteristics of rarefied nitrogen gas flows in microchannels are investigated using direct simulation Monte Carlo with improved pressure boundary conditions. The influence of aspect ratio and wall temperature on mass flowrate and wall heat flux in microchannels are studied parametrically. In order to examine the aspect ratio effect on heat and mass transfer behaviors, the wall temperature is set constant at 350 K and the aspect ratio of the microchannel varies from 5 to 20. The results show that as the aspect ratio increases, the velocity of the flow decreases, so does the mass flowrate. In a small aspect ratio channel, the heat transfer occurs throughout the microchannel; as the aspect ratio of the microchannel increases, the region of thermal equilibrium extends. To investigate the effects of wall temperature (Tw) on the mass flowrate and wall heat flux in a microchannel, the temperature of the incoming gas flow (Tin) is set constant at 300 K and the wall temperature varies from 200 K to 800 K while the aspect ratio is remained unchanged. Results show that majority of the wall heat flux stays within the channel entrance region and drops to nearly zero at the halfway in the channel. When Tw<Tin, under the restriction of pressure-driven condition and continuity of pressure, the molecular number density of the flow decreases along the flow direction after a short increase at the entrance region. When Tw>Tin, the molecular number density of the flow drops rapidly near the inlet and the temperature of the gas flow increases along the channel. As Tw increases, the flow becomes more rarefied, the mass flowrate decreases, and the resistance at the entrance region increases. Furthermore, when Tw>Tin, a sudden jump of heat transfer flux and temperature are observed at the exit region of the channel.