This article explores the divergent evolution trajectories within sectoral innovation system. A sectoral system is composed of three elements, i.e. knowledge and technology, actors and networks, and institutions. Since each of the three components could reveal multiple dynamics, different trajectories co-existing in the sector are able to be integrated shaped by the particular dynamics of the three components. Through investigating the evolution of two sub-sectors embedded in the Traditional Chinese Medicine industry in China, we find that sectoral development does not always follow single pattern but is able to be jointly pushed by the uneven development of different sub-sectors. The strategic policy supports towards a particular sector under such circumstance should therefore fully consider the heterogeneity within the sectoral system and foster the balanced development across different sub-sectors in the long term.