Small and medium-sized science and technology innovative enterprises have become an important organizational form of China's economic development, which has a huge impact on economy and social development. With the advent of the era of the strict taxation, it has realistic significance that small and medium enterprises carry out tax planning. This article defines the concept of the small and medium-sized science and technology innovative enterprises and tax planning, principles that should be followed and analyzes the problems that the enterprises may face in tax planning. And aimed at these problems, this paper puts forward the countermeasures and suggestions that enterprises implement tax planning from aspects of the preferential tax policy, tax management for daily business processing, coordination of production and financial, investment and financing activities and corporate strategic management.