Abstract: Green innovation is a new driving force for high-quality development, and the spatial differentiation of green innovation efficiency is related to higher-quality integration in the Yangtze River Delta. This paper selects the data of 41 cities in the Yangtze River Delta from 2006 to 2017, uses the SBM model to measure the efficiency of urban green innovation, using Theil index and Hurst index to describe the temporal and spatial characteristics of green innovation efficiency, and selects the Tobit model from “environment-economy-policy” three dimensions to systematically discuss its influence mechanism. The result showed that: (1) The volatility of urban green innovation efficiency in the Yangtze River Delta region is rising, regional differences are gradually decreasing, and the regional coordinated development trend is obvious. (2) Efficient “depressions” has appeared around some core cities in the Yangtze River Delta, and high-efficiency distribution areas have transformed from regions with superior natural endowments to regions with high technical and industrial structure. (3) The green innovation efficiency of cities in the central part of the Yangtze River Delta is at risk of continuing to decline. The eastern coastal zone and the cities in the outer circle of Jiangsu Province are the main areas of continuous growth, which are distributed in bands and rings. (4) Economic factors and policy factors have a higher degree of explanation for green innovation efficiency than natural factors. Factors such as urban economic strength, industrial structure, and environmental regulations play a particularly significant role, but the effects of each factor show phased differences. This has provided scientific support for formulating innovation-driven green development policies tailored to local conditions and promoting higher-quality integrated development in the Yangtze River Delta.