Collaborative innovation is the key to improving the overall efficiency of the innovation system. Based on the data of 280 prefecture-level cities in China from 2001 to 2020, the national innovative city pilot policy and the pilot policy of combining science and technology finance are regarded as a quasi-natural experiment. The gradual double difference model is used to empirically test the impact of the implementation of the dual pilot policy on urban innovation level. The results show that the combination of pilot policies can significantly promote the improvement of urban innovation level. The mechanism test reveals that the dual pilot policy has enhanced the level of urban innovation by promoting the agglomeration of risk institutions, improving the institutional environment and developing financial technology. Further analysis finds that the dual pilot policy has a collaborative innovation effect. Compared with the single pilot policy, the dual pilot policy can improve the level of urban innovation more effectively, and has a stronger impact on the cities that implement the innovative city pilot policy and cities in the non-eastern region. This paper explores the collaborative innovation effect of policy mix, and provides policy enlightenment for improving the urban innovation governance system.