The article considers the mathematical model describing the joint motion of a viscous compressible heat-conducting fluid and a thermoelastic plate with a fine two-level thermoelastic bristly microstructure attached to it. The bristly microstructure consists of a great amount of taller and shorter bristles, which are periodically located on the surface of the plate, and the model under consideration incorporates a small parameter, which is the ratio of the characteristic lengths of the microstructure and the entire plate. Using classical methods in the theory of partial differential equations, we prove that the initial-boundary value problem for the considered model is well-posed. After this, we fulfill the homogenization procedure, i.e., we pass to the limit as the small parameter tends to zero, and, as a result, we derive the effective macroscopic model in which the dynamics of the interaction of the ‘liquid–bristly structure’ is described by equations of two homogeneous thermoviscoelastic layers with memory effects. The homogenization procedure is rigorously justified by means of the Allaire–Briane three-scale convergence method. The developed effective macroscopic model can potentially find application in further mathematical modeling in biotechnology and bionics taking account of heat transfer.