The independent innovation of enterprises is influenced by financial constraints and tax incentives. It has important value that to study the impact of tax incentives on the incentive effect of independent innovation from the perspective of financial constraints is helpful to reexamine and improve the tax preferential policies in the field of innovation and alleviate the pressure of enterprise financial, and finally to stimulate the potential of independent innovation. The author analyzes the influence of tax preferential policies on the independent innovation of enterprises by DID method.The study shows that China's listed companies generally face the difficulties of financial constraints, and there are obvious areas, ownership and industry differences. The double tax preferential policies have the inhibitory effect on the independent innovation of the enterprise. The negative effect of the financial constraints will offset or even exceed the positive effect of the tax preference on the independent innovation of the enterprise, which makes the adjustment of the tax preferential policy difficult to produce the expected positive innovation effect. Accordingly put forward the corresponding countermeasures and solutions.