Abstract: The integration of industrial chain and innovation chain is an important measure to improve the toughness of industrial chain and the modernization level of industrial chain and supply chain. The development of traditional Chinese medicine industry in Anhui province has entered a new stage, but it is still difficult to integrate innovation chain and industrial chain in the process of development. This paper examines the integration efficiency of innovation chain and industrial chain of "Top ten Anhui pharmaceutical" enterprises by coupling coordination degree model and combining TOPSIS and RSR. The results showed that there was a high correlation between the two systems of traditional Chinese medicine innovation chain and industrial chain in Anhui province, but the coupling coordination degree was low, the coupling was at a low level and there were obvious regional differences. Based on this, it is proposed that enterprises and other innovation subjects should follow the law of integrated development of innovation chain and industrial chain to promote the two-way integration of the two chains, explore the integrated development of regional innovation chain and industrial chain according to the development level of regional two chains, and promote the collaborative innovation and development of production, university and research, in order to further promote the high-quality development of traditional Chinese medicine industry.