Based on a platform of a high pressure air compressor, the transfer function matrix of the air supply subsystem for high pressure proton exchange membrane fuel cell (PEMFC) is identified and then the air flow and back pressure is decoupled via feed forward compensation decoupling control technique. Both the results of experiment and simulation show that the proposed controller can really achieve the decoupling control of air flow and back pressure, and it also has good robust performance in a large range of working condition.