The slowdown of China's economic growth in the middle-income stage has caused widespread concerns. Based on the analysis of economic structures to explain the downward trend of economic growth, this study expanded the Solow-Swan model to investigate the structural imbalances and evaluated their impacts during the structural transformation in different stages and regions on the economic downturn. Considering the processes of production, distribution, and consumption, six structures were chosen for national and prefecture-levels in China from 1997 to 2017, including sectoral structure, population structure, investment and consumption structure, import-export structure, urban-rural income structure, and financial structure. The study found that China's comprehensive economic structure was significantly different before and after the middle-income stage, and structural bonus tended to decline. Structural imbalance presented a U-shaped pattern of decreasing first and then increasing, and the impact on economic growth underwent stages of suppression-promotion-suppression. There was a significant difference in the imbalance of six sub-structures and their impacts; furthermore, in the four regions of east, center, west, and northeast the observations were very different. Taken together, the imbalance of economic structure and economic transformation coexisted, and the economic growth slowed down. Based on the experiences from China, this paper provided some evidence for promoting structural optimization and transformation.