The strengthening of urban innovation capacity has emerged as the main force behind the promotion of the high-quality development in China because it is a significant carrier of regional innovation. This work uses the multi-time point difference approach to study the synergistic effect, mechanism, and heterogeneity among the pilot policies of national innovation city, low-carbon city and smart city based on the panel data of 282 cities from 2001 to 2016. The findings demonstrate that (1) The national innovative city pilot policies, low-carbon city pilot policies, and smart city pilot policies have a significant effect on the improvement of urban innovation and show a synergistic effect. (2) With the help of government investment in science and technology and the construction of an innovation platform, the pilot policies of smart cities and innovative cities show a superposition effect; in addition, through the upgrading of industrial structure, the green technology innovation, public participation, low-carbon urban pilot policy, and the innovative city present the supplementary effect. (3) From the perspective of heterogeneity, the superposition and supplementary effects of lower administrative level cities are better. The effect of policy synergy overlay is the largest in the eastern region, whereas the effect of policy synergy supplement is stronger in the eastern and western regions than in the central region. The robustness test supports the conclusion of this paper. This paper analyzes the collaborative innovation effect of urban pilot policies, which can provide ideas for the combination design of policy tools.