At the present time, there are many problems associated with the cost accounting system of China’s state-owned scientific research institutes. It becomes more and more important to establish a cost accounting system of state-owned scientific research institutes conforming to the science and technology development laws and China’s national conditions. The present situations of the existing accounting system of state-owned scientific research institutes in China and abroad are analyzed; the major problems within the accounting system of China’s state-owned scientific research institutes are explored. Then a cost accounting framework system suiting to China’s national conditions is proposed. It has both theoretical and practical significance for improving management of sci-tech innovations and deepening sci-tech innovations.