This paper uses the industrial enterprise database, customs database, enterprise patent database from 2000 to 2014 and China’s input-output table in 2007 to verify the impact of RMB appreciation on manufacturing enterprise innovation from the perspective of industrial chain. The research results show that the appreciation of RMB can significantly improve the innovation capability of enterprises, and the industrial chain plays a heterogeneous role in it: that is, enterprises will show the difference between“quantity”and“quality”of innovation due to their position in the industrial chain. The appreciation of RMB plays a stronger role in promoting the innovation quality of upstream enterprises, but has no obvious impact on the innovation quantity. The mechanism analysis shows that the increase of imported intermediate goods brought about by the appreciation of RMB will form inter-industry technology spillover effect and intra-industry competition effect in the industrial chain, which will have an important impact on the enterprise innovation model; The upstream industry enterprises show“quality leading effect”in the whole industry chain, providing a constructive direction for enterprises to improve their own innovation by using the industry production network effect under the“double cycle”development pattern.