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This study aims to investigate the influence of the financial system (financial development and financial structure) on firms' innovation efficiency in China.

This study employs country level data of capital markets and financial institutions along with innovation data from 18 high-tech industries in China spanning the 2009–2016 period, and the stochastic frontier analysis (SFA) is applied to explore how financial development and financial structure affect the innovation efficiency of these industries.

Results show that financial development influences firms' innovation efficiency positively and the capital-market-based financial structure has a positive impact on innovation efficiency of high-tech industries. Furthermore, when the high-tech industries are grouped into five sub-industries, the results show that financial structure had different effects on the innovation efficiency in each sub-industry.

This work contributes to the empirical research on considering the influential factors of innovation efficiency from the perspective of financial system. This paper also extends the existing literature by the different influences of financial system on innovation efficiency in each sub-industry of Chinese high-tech industries.