In nature, essentially, almost all the particles move irregularly in non-static media. With the advance of observation techniques, various kinds of new dynamical phenomena are detected, e.g., Brownian non-Gaussian diffusion. This paper focuses on the dynamical behavior of the center of mass (CM) of a polymer in non-static media and investigates the effect of polymer size fluctuations on the diffusion behavior. First, we establish a diffusing diffusivity model for polymer size fluctuations, linking the polymer size variation to the birth and death process, and introduce co-moving and physical coordinate systems to characterize the position of the CM for a polymer in non-static media. Next, the important statistical quantities for the CM diffusing diffusivity model in non-static media, such as mean square displacement (MSD) and kurtosis, are obtained by adopting the subordinate process approach, and the long-time asymptotic behavior of the MSD in the media of different types is specifically analyzed. Finally, the bivariate Fokker–Planck equation and the Feynman–Kac equation corresponding to the diffusing diffusivity model are detailedly derived and solved through the deep backward stochastic differential equation (BSDE) method to confirm the correctness of the derived equations.