In the traditional aerodynamic design of aircraft/engine integration, engine system was usually modeled by the flow-through nacelle, but it is very different that the simulation of intake and exhaust effects by flow-through nacelle compared with actual engine work conditions. To improving ability on this problem, the research had be done about the interference of the powered effects to high speed buffet characteristics on the cruise configuration of a civil aircraft with method of solving RANS equations on multi-block structured grid system. Firstly, it was verified that the powered effects can be modeled by intake and exhaust boundary conditions. Secondly, the method that it can be used to judge buffeting onset is given by comprehensive consideration of calculation accuracy and efficiency in the preliminary design stage. Analysis shows: the powered effects had a bad interference to buffeting onset that was designed based on flow-through nacelle at the cruise Mach number, lift coefficient of buffeting onset was reduced about 1.3% of total. We suggest that the effects of power of engine should be considered when checking buffet constrain for the configuration designed based on the flow-through nacelle.