The innovation collaboration between leading and following enterprises in the emerging technology innovation ecosystem around emerging technology breakthroughs is an important way to promote the rapid cross-fertilisation of emerging technologies, promote the extension of the industrial chain to the high-end, and accelerate the development of new productivity. Based on the technological asymmetric dependency situation in the process of emerging technology innovation collaboration, we construct an evolutionary game model of innovation collaboration strategies between leading and following enterprises, analyse the strategy choices of both parties under the original market mechanism and the reward and punishment protection mechanism, as well as their dynamic evolution mechanism, and verify the key influencing factors through numerical simulation. The results of the study show that the collaborative decision making of emerging technology innovation between the leader and the follower is mainly influenced by universal factors such as contractual compensation, risk loss of core technology leakage, "free rider" gain and technology gain coefficient; the opportunity cost loss of the follower due to asymmetric dependence on technology, the potential of technology absorption and the technological advantage of the leader drive the two parties to move to a higher level of technological innovation, which is the most important factor for the collaborative decision making of emerging technology innovation.