Abstract: Green innovation, as the combination of the two national development strategies of innovation-driven and green development, has gradually become the focus of attention of all sectors of society. Regions are carriers of green innovation. Accurate evaluation of regional green innovation capabilities and analysis of the spatial characteristics of interregional green innovation capabilities will help close-knit regions achieve higher-quality integration. This article comprehensively uses collinearity-variance coefficient analysis method to screen the evaluation indexes involved in the existing literature, and establishes evaluation system of regional green innovation capacity, which consists of three first level criteria layers as green innovation input, green innovation output, and green innovation foundation, and 46 evaluation indicators. Then, it is based on the data of 26 cities in the Yangtze River Delta Urban Agglomerations in 2015, using exploratory spatial data analysis methods, using ArcGIS 10.2 and GeoDa1.12 software tools to analyze the spatial pattern and spatial relationship characteristics of the green innovation capacity of the Yangtze River Delta Urban Agglomerations. Empirical results show: (1) The regional green innovation capacity evaluation index system constructed based on the collinearity-variance coefficient index screening model, reflects 92.1% original information by 62.2% index, and can objectively test and measure the level and problems of green innovation capacity in the research area. (2) The green innovation capacity of the Yangtze River Delta Urban Agglomerations is generally low and unevenly developed. The average score of the 26 city indexes is only 0.225. The Shanghai city with the highest score is 7 times as much as the last one Tongling city. The urban green innovation capacity and regional synergy innovation needs to be improved. (3) The cities with relatively high green innovation capacity are mostly distributed along the Yangtze River or along the coastline, and have a zigzag distribution in space. The green innovation capacity of the Yangtze River Delta Urban Agglomerations shows a certain spatial dependence and spatial connection, which confirms the feasibility of green coordinated and innovative development among cities in the Yangtze River Delta Urban Agglomerations to achieve higher quality integration.