Urban agglomerations are becoming an important spatial carrier for China’s industrialisation and new-type urbanisation, and an important engine to drive the national economic development, and regional economic differences based on urban agglomerations have also become a new feature of China’s regional differences in the new period. Based on the urban agglomeration perspective, we quantitatively measure China’s regional economic differences from 2001 to 2020 through the two-stage nested decomposition method of the Theil Index, and analyse the evolutionary characteristics of the economic differences within the 19 urban agglomerations in the country by decomposing them into four major regions: East, Central, West and Northeast, and the differences between the urban agglomerations within the regions and the economic differences within the urban agglomerations. The study found that: (1) Overall the overall differences of the region with urban agglomerations as the core were gradually shrinking. In terms of the trend of changes in the differences at all levels, the economic differences between regions and within urban agglomerations were significantly reduced, and the changes in the economic differences between urban agglomerations were not obvious. In terms of contribution rate, the contribution rate of intra-urban agglomeration differences had always remained at a high level, reaching about half of the overall economic differences in the country, and was the primary contributing factor to the overall economic differences. (2) In terms of absolute differences, the economic differences among urban agglomerations in the four regions showed a clear pattern of “East > West > Central ≈ Northeast”. (3) The intra-cluster economic differences of each urban agglomeration in 20 years were at different levels and showed a differentiated trend of evolution, and the areas with relatively more prominent intra-cluster economic differences were the Pearl River Delta urban agglomeration in the east, and the Lan-xi urban agglomeration and the North Slope of Tianshan Mountain urban agglomeration in the northwestern region. The economic differences of urban agglomerations are the result of a variety of factors, and the reasons for the formation of regional economic differences are analysed from the factors of economic location, national regional development policies, human resource factors and high-speed traffic differences within the urban agglomerations.