The invention discloses a method for integrally designing a high-accuracy varying temperature microwave black body calibration source. According to the method, the electromagnetic characteristics and thermodynamic characteristics of the microwave black body calibration source are jointly subjected to optimal design; firstly the electromagnetic characteristics of a black body emissivity index are optimized, and the optimal design is carried out according to the precedence order of a black body wedge dimension proportion, a wedge array form, a wave-absorbing material coating thickness and a wave-absorbing material electromagnetic parameter, so that the emissivity of the black body calibration source achieves more than 0.999; then the thermodynamic characteristics are optimized, the optimal design is carried out by mainly optimizing the precedence order of the black body wedge dimension proportion, the wedge array form and the wave-absorbing material coating thickness; finally the temperature measurement position of the microwave black body calibration source is provided, so that the uncertainty degree of output microwave brightness temperature is ensured to be less than 0.05 K. The method disclosed by the invention can effectively increase the design efficiency of a high-accuracy microwave brightness temperature standard output by the varying temperature microwave black body calibration source and achieves the convenience for practical application.