Giving the fact that manufacturing industry is still the engine of economic development in developing countries, China pays special attention to the development of manufacturing industry, especially the hi-tech industry. This paper takes the manufacture of medicine as an example, aiming to investigate the development status of the manufacture of medicine in Yangtze River and Pearl River Deltas, which are China's major manufacturing centers. In this context, the dynamic index system composed of R&D Stage, Production Stage and Output Stage is established and the Gray CorrelationAnalysis Model is applied in evaluating. The results indicate that there is a gap between Yangtze River and Pearl River Deltas. The capacity of turning R&D and innovation input into output is important to promote the development of the manufacture of medicine and the synergy effect of the industry value chain can’t be ignored.