Preferential income tax policy is an important means of stimulating firms’ innovation, and innovation efficiency is a key factor determining firms’ long-term performance. The analysis and evaluation of the effect of current policies on firms’ innovation efficiency is an important procedure for testing policies. Based on a deep investigation into 195 firms in Shaanxi Province, this paper uses the SFA model and finds that pretax additional deduction policy can increase the innovation efficiency of high-tech firms, but has no effect on non-high-tech firms. Based on matching samples, this paper uses difference-in-difference model and analyzes the effect preferential income tax policy applied to high-tech enterprises, and finds that this policy cannot improve high-tech firms’ innovation efficiency significantly. Finally, this paper proposes suggestions for improving the real effect of current policies.