Abstract: With the continuous development of the economy, China has entered a new era of high-quality development. In the new stage of Chinese development, the main direction is to vigorously develop new quality productive forces driven by innovation based on local conditions. For a large economy like China, the real economy has always been the foundation of the entire economic framework, and industrial production is the main component in the real economy. Therefore, supporting and incentivizing industrial innovation has become a major gain for policy makers in the process of building an innovative country. The government has two methods to incentivize industrial innovation, including explicit and implicit fiscal expenditure of science and technology. Firstly, the government can support industrial innovation by directly injecting fiscal funds into industrial enterprises, which is known as explicit fiscal expenditure of science and technology. Secondly, in the process of market-oriented reforms, enterprises are the main body of innovation, so the expenditure methods for supporting industrial innovation more prefer to the ways of market. Therefore, implicit fiscal expenditures of science and technology in the form of R&D expense additional deduction and high-tech enterprise tax reduction are more applicable in more scenarios. Currently, in the China’s Public Finance Model, fiscal expenditure of science and technology for promoting industrial innovation has presented a new feature as follows: the implicit fiscal expenditures of science and technology in the form of tax reductions have greatly exceeded the explicit fiscal expenditures of science and technology. Direct effect of science and technology expenditure by the public sector in supporting industrial innovation activities is increasing industrial R&D innovation input because enterprises are the main body of innovation as described above. However, its actual economic value is bringing about a significant increase in innovation output. Using data from China’s industrial sectors and taking the number of invention patent applications as an indicator of innovation output, this paper estimates the impact of explicit fiscal expenditure in the form of direct government funding and implicit tax expenditure in the form of R&D expense additional deduction and high-tech enterprise tax reduction on industrial innovation output through various methods. This study finds strong and robust evidence that the two forms of implicit fiscal science and technology expenditure have no significant impact on industrial innovation output, and their combined effect is also not significant. Contrastively, R&D expense additional deduction and high-tech enterprise tax reduction have a significantly positive impact on internal R&D expenditure of industrial sectors, with elasticities of 22.38% and 7.9%, respectively. Therefore, industrial enterprises have a strong tendency of “strategic catering” innovation when facing tax reduction incentives. There is evidence that explicit fiscal science and technology expenditure has a significantly positive impact on industrial innovation output, but it is not robust. Since industrial enterprises do not significantly increase internal R&D expenditure due to government inputs fiscal science and technology funds, there is no incentive for industrial enterprises to engage in “strategic catering” innovative behaviors due to explicit fiscal science and technology expenditure. Based on the theoretical analyses and empirical tests, to increase the value of the market in the allocation of innovation resources, the form of government support for industrial innovation should prefer to implicit tax subsidies rather than explicit fiscal expenditures. However, the “strategic catering” innovation behavior of market entities for tax reduction is not conducive to the effective utilization of innovation resources. This dilemma is a major obstacle to support industrial innovation by using the fiscal funds. Eliminate this bottleneck requires the integration and coordination among technology policies, industrial policies, and fiscal and tax policies in the future.