In order to enhance the thermal stability and thermochromic properties, three kinds of VOx-based thin films with different structures (single-layer, triple-layer and multi-layer, respectively) were designed in this study. All of them were prepared by room-temperature reactive magnetron sputtering and subsequently rapid thermal annealing (RTA) in nitrogen atmosphere. The optical properties and microstructure of VOx-based thin films were investigated. The results reveal that all samples are ascribed to pure VO2 (M), and the VOx-based thin films exhibit superior thermochromic properties with the solar modulation (Delta T-sol) up to 12.75%, 15.65% and 18.02%, respectively. The phase transition temperature (T-c) is as low as 54 degrees C for multi-layer thin films without doping, which indicates that the film design could effectively enhance optical switching and depress the T. After thermal treatment in the air, the phase of V2O5 appeared at 325 degrees C, 275 degrees C and 375 degrees C for single-layer, triple-layer and multi-layer thin films, respectively, which indicates the multi-layer thin films show the best thermal stability. According to the degradation mechanism in this paper, the unbalance of interfacial stress and oxygen vacancies in VOx thin film accelerated the oxidation process, which results in the disappearance of thermochromic properties. Furthermore, the multi-layer thin films still show superior Delta T-Sol of 16.56% and T-c of 56 degrees C, when it was taken out at 400 degrees C and cooled quickly in air. Meanwhile, the annealing period could be reduced by 75% in comparison to cooling in vacuum chamber. Our research set forth a new avenue in enhancing the thermal stability and production efficiency, which can promote the practical applications of VOx-based thin films.