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The paper analyzes the effect of environmental uncertainty on corporate technological innovation from the perspective of an innovation value chain under the institutional background of China. This paper not only discusses the intermediary effect of agency problems on environmental uncertainty and corporate technological innovation but also deeply explores the influence of information transparency, government subsidies, and other mechanisms to alleviate agency problems on environmental uncertainty and corporate technological innovation. We use the data of listed companies in China from 2008 to 2019 as the research sample, and the results show that, in general, environmental uncertainty has a negative effect on both input and output of technological innovation, and the negative effect can last for two years. Further research shows that the agency problem has an intermediary effect on the environmental uncertainty and corporate technology innovation, and the environmental uncertainty aggravates the agency problem, which hinders the input and output of corporate technology innovation. As an important mechanism to alleviate the agency problems, information transparency and government subsidies can effectively alleviate the agency conflict, thus reducing the inhibition of environmental uncertainty on the input and output of technological innovation. Our findings contribute to the discussion of driving factors for technological innovation in the context of China’s system. Our results provide useful insights into the link between environmental uncertainty and corporate innovation for economic academics and practitioners alike.