Summary form only given. Since the 1990s began, profound changes have taken place in the world pattern, and the competition in science and technology is becoming the core of international strife. Therefore, R&D funds have become the essential condition so that a nation acquires long-term competitive advantage and international competitiveness. It is very important for a country to timely adjust its structure of R&D funds on the basis of its characters and national need. Based on this view, this paper compares the three aspects of structural transformation process, i.e. the structure of R&D funds by source, the structure of R&D funds by performing sector, and the structure of R&D funds by character of work in China and the US. The main conclusions are listed as follows: (1) the structure of R&D funds by source in the US has gone through three phases from government-dominance type to industry-dominance type since the 1960s. The same trend happened in many other developed countries. In contrast, the structure of R&D by source in China still belongs to typical government-dominance type. (2) The structure of R&D funds by performing sector in the US and many developed countries turned traditional "single-assistant" type into "double-assistant" type in order to fit the new technology-economy paradigm shift. However, in China the structure of R&D by performing sector just pertains to an institute's dominance far away from single-assistant type. (3) The structure of R&D funds by character of work in the US stresses the stability of R&D system and has a high share of basic research. But basic research in China is very weak.