In the new era, the key measure to accelerate the construction of smart city, so as to promote the modernization of urban governance system and governance capacity, is to establish a good urban innovation ecosystem, and guide its continuous evolution to the direction of the highest efficiency and the best performance. Focusing on solving the practical problem of “how the urban innovation ecosystem evolves”, this paper develops a NK algorithm using BP neural network and DEMATEL method. First, through literature research, constructing the urban innovation ecosystem including five subsystems of innovation talents, innovation subjects, innovation resources, innovation environment and innovation network. Then, taking Beijing as an example, the weights and the number of epistatic relationships of each subsystem in its innovation ecosystem are calculated by BP neural network and DEMATEL method, and the NK model is modified; on this basis, the fitness values corresponding to different states of the system are calculated using MATLAB software, and the optimal evolution path of Beijing innovation ecosystem is determined through the comparison of 100,000 simulation results. The results show that the optimal evolution path of Beijing's innovation ecosystem is to create a favorable environment and culture for innovation first; then increase the input of innovation resources; and then promote the development of innovation network assets; on this basis, cultivate, attract and retain innovative talents; and finally strengthen the construction of innovation subjects.