Pressure　and　mass　flow　control　in　fuel　cell　air　supply　systems　highly　affect　the　dynamic　performance,　reliability,　and　efficiency　of　proton　exchange　membrane　fuel　cell　vehicles　(FCVs).　However,　the　coupling　effect　between　pressure　and　mass　flow　makes　their　control　difficult　and　can　seriously　compromise　the　performance　of　proton　exchange　membrane　fuel　cells　(PEMFCs).　In　this　article,　the　optimization　diagonal　matrix　decoupling　(DMD)　is　proposed　to　avoid　the　occurrence　of　detrimental　operating　conditions　and　improve　performance.　This　study　includes　data-driven　modeling　of　the　air　supply　system　with　transfer　functions　and　the　analysis　of　the　coupling　mechanisms　between　pressure　and　mass　flow.　The　simulation　results　show　that　the　proposed　strategy　has　good　disturbance　rejection　and　low　coupling　between　flow　and　pressure.　Compared　with　conventional　DMD,　the　standard　deviation　(std)　of　the　relative　control　error　of　flow　and　pressure　can　be　reduced　by　9.7%　and　14.4%　in　the　proposed　strategy.　The　new　contribution　of　this　article　is　to　reveal　the　coupling　mechanism,　which　can　be　used　to　guide　the　design　of　decoupling　control　strategies　designed　for　air　supply　systems　of　fuel　cell　engines　in　FCV.