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The electromagnetic performance of an active phased array antenna (APAA) is obviously degraded because of structural distortion caused by thermal power consumption and exterior load. The coupled structural-electromagnetic-thermal (SET) model of APAA is developed on the analysis of the phase difference of radiating elements in the aperture field caused by structural displacement including load-displacement and thermal distortion of structure. Based on the cascade coupled finite element analysis of antenna structure, thermal distortion and other structural distortions are obtained. The coupled SET model is verified by analysing the degradation of the electromagnetic performances of a planar hexagonal APAA operating under different temperature distributions and structural constraints.