As the “main engine” of high-quality development of enterprises, technological innovation is an inevitable choice to realize industrial structure adjustment, transformation and upgrading. Taking the panel data of 226 listed companies in software and information technology industry on growth enterprise market from 2015 to 2018 as the research object, an inquiry has been made into the impact of R&D intensity and R&D density on the financing structure, with a focus on the regulatory effect of income tax incentives on the above-mentioned relationship. It is found that R&D intensity and R&D density are significantly negatively correlated with financing structure, with income tax preference effectively promoting the debt level of innovation investment as well as alleviating the impact of R&D intensity and R&D density on financing structure. Therefore, it is suggested that enterprises establish a scientific and innovative fund financing mechanism and reasonably allocate resource elements to optimize enterprise financing structure; our nation should consider how to reduce the inhibitory effect of technological innovation investment on debt financing from many aspects.