Scientifically justifiable spatial structure can not only promote the efficient use of regional resources, but can also effectively avoid "urban diseases", such as traffic congestion, housing shortage, resource scarcity, and so on. It is the "regulator" and "booster" of regional development. Firstly, this paper measures the spatial structure of the Yangtze River Economic Belt from the four dimensions of scale distribution, central structure, spatial connection, and compactness: Gini coefficient of urban scale, urban primacy, regional economic linkage strength, and spatial compactness. Secondly, the optimized Super-Slack Based Measure-Undesirable model is used to evaluate the sustainable development status of the Yangtze River Economic Belt. Finally, a sustainable development correlation analysis model based on regional spatial structure is constructed. Based on the overall perspective of the Yangtze River Economic Belt and the individual perspective of 11 provinces and cities, the relationship between the spatial structure of the Yangtze River Economic Belt and sustainable development is analyzed. It is found that the impact of the four spatial structure indicators on the sustainable development level of the Yangtze River Economic Zone is relatively stable in five different periods. The ranking results are as follows: Gini coefficient of urban scale > urban primacy > regional economic linkage strength > spatial compactness.