The policies for research and development expenses pre-tax deduction is one of the important technological innovation preferential policies, however the statistical data shows that the practice effect of the policy is not quite ideal. There are three main problems, that is, firstly the R&D expenses range affected by the policy is narrow, the content of R&D expenses is not clearly defined, and cost audit and regulatory requirements are not clear; secondly the tax task pressure around the local tax authorities and the poor understanding of the policy caused the bad practice effect; thirdly the weak R&D expenses management and the poor internal communication inside enterprises also cause the bad practice effect. In the end, some suggestions are given to solve these problems, such as conforming to financial accounting standards, resolving the differences of the tax revenue through transfer payments, establishing three dimensional accounting system involving subject-project-department, etc.