The study applies the social cooperation network and multi-period DID to identify the conduction path and effect of innovative-city pilot policy on IUR collaborative innovation in 26 YRD cities during 2005–2020. The IUR collaboration innovation has made significant progress in YRD. Simultaneously, the IUR cooperative intensity and control capability of cooperative network of YRD cities have increased gradually. However, the IUR R&D efficiency and IUR transformation efficiency both haven’t reached the optimal level in YRD, and the transformation efficiency is always less than R&D efficiency. The pilot policy has a positive effect on improving IUR innovation efficiency. The policy effects for provincial capital cities are greater than those for non-provincial capital cities. Provincially, the pilot policy on IUR collaborative innovation efficiency reaches highest in Zhejiang and lowest in Jiangsu. The IUR cooperative intensity and control capability of cooperative network have partial intermediary effect on pilot policy.