Abstract: As an important and effective policy tool for intervening and stimulating enterprise R&D investment, tax favors are used by more and more countries, and there is a strong evidence in theory and practice. Firstly, in order to evaluate the effect of China's preferential tax policies of enterprise R&D investment, the author established a mathematical model based on the horizontal innovation which composed of R&D sector，final goods production, intermediate goods production and so on. From derivation and analysis of the model, we found that plus tax deduction rate and corporate R&D investment is related, and when plus pre tax deduction remained unchanged and R&D expense deduction scope, the enterprise suitable to the high tax rate will invest more funds in R&D activities. Secondly, we select the data from the Shanghai and Shenzhen listing Corporation to establish a Difference-in-Difference model to evaluate the effect of the tax favor policy implemented in 2013. The study found that the tax favor policy for the country's key support and small and micro high-tech enterprise R&D investment has not reached the expected incentive effect, which is consistent with the conclusion of the mathematical model. Finally, a brief summary of the full text and put forward relevant policy recommendations.