Abstract:National independent innovation demonstration zones are important carriers for implementing the innovation-driven development strategy, and they play a pioneering, exploratory, and demonstrative role in promoting independent innovation and the development of high-tech industries.[Methods/Process] Using the DEA model and entropy weighting method, an innovation performance evaluation index system is constructed from two dimensions: innovation transformation efficiency and output efficiency. The national independent innovation zones are comprehensively evaluated, and the spatio-temporal differences are analyzed. A econometric model with virtual variables is constructed to explore the effects of the construction of the Lanzhou and Baiyin independent innovation zones on optimizing and upgrading the industrial structure. The study found that: (1) During the observation period, there were significant differences in the level of innovation performance in the national independent innovation demonstration zones, and they showed agglomeration characteristics in spatial distribution. The innovation performance of the eastern regions" zones surpassed the national average and the central and western regions. (2) Overall, the innovation performance level of the Lanzhou and Baiyin independent innovation zones was relatively low, at the "low efficiency-low benefit" level. However, since their approval, both innovation efficiency and benefits have shown an overall upward trend, and there are differences in the innovation performance level between the two zones, Lanzhou and Baiyin, which are the main construction entities. (3) The declaration and construction of the Lanzhou and Baiyin independent innovation zones have significantly promoted the upgrading of the industrial structure in Gansu Province. However, this effect is temporary and has a short-term impact. The impact at the initial stage of declaration is significant, while the impact on the advanced and rationalized industrial structure is heterogeneous. Finally, based on the research findings, the path to enhancing the innovation performance of the Lanzhou and Baiyin independent innovation zones and promoting the upgrading of the industrial structure is proposed, focusing on core technology breakthroughs, the cultivation of innovative entities, the development of an innovative environment, and open innovation cooperation.