Obtaining the input load presents a significant challenge for system identification problems with time-varying characteristics in aerospace engineering. Therefore, the modal parameter is determined through output-only identification techniques. Considering rapid time-varying characteristics in thermal environment, a Recursive Subspace Method (RSM) is used to enhance the precision of identifying modal parameters. A three-degree-of-freedom system with time-varying stiffness is first investigated to validate the identification method. The effect of noise on the robustness of the algorithm is discussed. Then, the experimental investigation is undertaken considering a composite beam under a time-varying thermal environment though the thermal-vibration experimental system. Experimental results indicate that the change of structural modal frequencies under variable temperature environment is mainly affected by the thermal stress induced in the structure. Comparing the experimental and simulation result, the output-only identification approach has good efficiency and convergence for time-varying system.