Abstract: This article takes Shanghai FTZ and Zhejiang FTZ in the Yangtze River Delta as examples. It uses panel data from 2008 to 2019 of the cities they are located in and 47 prefecture-level cities around them, first adopts the spatial social network analysis method to filter the processing group and the control group, then separately constructs the Heterogeneous DID model from the perspective of comprehensive policy and the DDD model from the perspective of policy space segmentation, to conduct an in-depth investigation and evaluation of the spillover and superposition effect on regional economic development under “spatial linkage and interaction of institutional innovation between the two FTZs. The study finds that not only the respective institutional innovations of the FTZs have significant heterogeneous spillover effects on the economic development of surrounding regions, but the “linkage and interaction of institutional innovation” between the FTZs also have two-dimension spillover and superposition effect in time and space for the economic development of the intermediate region. Moreover, the quantitative evaluation also shows that the spillover and superposition effect received by the intermediate region is much greater than the pure spillover effect of a single FTZ on the surrounding areas. Further analysis of heterogeneity shows that the economic spillover effects of FTZs on provincial capitals, inland cities, geographically adjacent cities, and big cities are more significant.