Localized severe non-synoptic winds, such as downbursts and tornadoes, cause frequent structural failures of the electric transmission lines worldwide. This paper aims to develop an analytical approach to evaluate the extreme non-stationary dynamic response of transmission towers under downbursts in frequency domain. First, the empirical models of time-varying mean wind and non-stationary fluctuating wind of moving downbursts are introduced to deduce the transient wind loads on transmission towers in time domain. The closed-form frequency domain solutions of non-stationary fluctuating downburst wind-induced response of transmission towers are derived based on the pseudo excitation method. Furthermore, through the up-crossing extreme value theory, the probability distribution of the non-stationary extreme response is studied. Finally, the peak factors of the non-stationary and the equivalent stationary theoretical methods are compared based on the proposed equivalent stationary extreme value distribution for engineering application. The proposed theoretical framework is validated by stochastic sampling simulation and finite element analysis. It is found that the proposed theoretical framework can accurately assess the extreme value responses of transmission towers under non-stationary moving downbursts.