Effective boundary condition is one of the most critical problems in the computation of micro-channel flows with direct simulation Monte-Carlo (DSMC) method. In the present work, the implementation of DSMC with specified pressure boundary condition (PBC) was discussed in detail. The variations of gaseous local pressure, temperature and number density of the particles caused by the temperature difference between channel walls and gas were presented. It was found that with the increase of both gaseous compressibility and rarefaction, the pressure distribution along micro-channel became more nonlinear. Heat transfer occurred almost only at channel inlet and outlet, and the average wall heat flux increased almost linearly to the inlet-to-outlet pressure ratio. The computational results also showed that PBC was more suitable for the simulation of micro-channel flow problems than the conventional velocity boundary condition (VBC).