GaN　Schottky　diodes　exhibit　great　potential　for　high　power　THz　frequency　multipliers.　This　paper　presents　thermal　characterization　results　of　GaN　Schottky　diodes　in　the　frequency　multipliers　with　flip-chip　configuration.　Common　models　of　the　different　Schottky　diode　multiplier　chip　layouts　are　analyzed　with　3-D　thermal　simulators.　The　thermal　resistance　results　show　that　the　GaN　Schottky　diodes　chips　have　evident　advantage　in　thermal　management　compared　with　GaAs　chips.　The　differences　of　n-anode　Schottky　diodes　chips　in　thermal　effect　are　investigated　in　detail.　The　impacts　of　solders　and　filter　substrate　on　thermal　resistance　are　shown,　which　indicate　the　the　filter　substrate　with　high　thermal　conductivity　will　improve　the　performance　of　the　THz　frequency　multipliers　obviously.