Abstract: To evaluate the green innovation efficiency of the Yangtze River Economic Belt accurately, this paper took environmental heterogeneity, decision-making unit heterogeneity, and all optimal weighting schemes into consideration. We constructed a double heterogeneity DEA interval cross-efficiency model and proposed the concept of a single heterogeneity DEA interval cross-efficiency evaluation. The green innovation efficiency of 95 cities in the Yangtze River Economic Belt from 2013 to 2020 was evaluated. The results were shown as follows: (1) During the period of inspection, no matter whether under double heterogeneity or single heterogeneity, the Yangtze River Economic Belt's overall green innovation efficiency had not yet reached a state of effectiveness. If examined in single heterogeneity, a clear upward trend and stage characteristics were shown. (2) In the event of double heterogeneity, the green innovation efficiency of the downstream areas needed to be more compatible with the levels of urban development. (3) Under single heterogeneity, the efficiency of green innovation had a significant spatial distribution, which displayed that the downstream areas were better than the midstream areas, and the midstream areas were better than the upstream areas. (4) Under dual heterogeneity, the green innovation efficiency of Suining was ranked as the first in the upstream areas. The performance of the green innovation efficiency of Shaoyang was the best in the midstream areas. Meanwhile, in the downstream areas, Bozhou had the best green innovation efficiency. In the station of single heterogeneity, Suining's green innovation efficiency was the highest. Finally, based on the above conclusions as well as the Yangtze River Economic Belt's regional locations and stages of urban development, certain suggestions were put forward to improve the efficiency of green innovation in the Yangtze River Economic Belt.