Based on the time-dependent matrix fraction polynomial model of transfer functions, the time-frequency-domain parametric model of linear time-varying structures is presented in this article. Furthermore, based on the time-frequency-domain parametric model, through adapting the current popular least square complex frequency-domain method of modal parameter estimation for linear time-invariant structures into the time-frequency domain, a matrix fraction polynomial model-based least square estimation method of modal parameters for linear time-varying structures in the time-frequency domain is presented. In addition, to reduce the unacceptably computational consumption of the time-frequency least squares, this article presents a reduced normal equation-based solution for the least square problem. Finally, the two 3-DOF simulation examples with the varying mass illustrate the influence of the constraints on the unknown parameters to the estimation results, discuss the characteristics of the proposed method and validate the proposed method itself and its potential applications.