In the first part of this work (Part I), we presented and validated the DSMC-HFS method, which can be used to deal with heat flux specified boundary conditions in DSMC simulations. In this article, the method is applied to demonstrate the general properties of rarefied diatomic gaseous flow in a microchannel under uniform heat flux boundary conditions. The effects of wall heat flux on gaseous flow and heat transfer characteristics are investigated numerically and discussed in detail. It can be concluded from the present research that gaseous rarefication and compressibility increase with the increase of the wall heat flux. Gas acceleration at higher wall heat flux is more obvious than that at lower wall heat flux. The high wall heat flux reduces the mass flow rate and elevates the heat transfer ability except at the channel inlet.