A Multi-airport Logistics System (MLS) involves the logistics development of multiple airports in an urban agglomeration. Calculating spatial differentiation in MLS and examining its characteristics have theoretical and practical value. Based on MLS, we established an index system and applied the entropy-criteria importance through the intercriteria correlation weighting method to data from 2019 to evaluate the development and spatial differentiation of multi-airport logistics in four Chinese urban agglomerations in three dimensions: logistics resources, service chains, and market demand. The results showed the following: (1) The Guangdong–Hong Kong–Macao Greater Bay Area showed logistics resource-type development. (2) Given its considerable market demand and service support, the Yangtze River Delta ranked first in the service-chain aspect. (3) The market-demand performance of the Chengdu–Chongqing Double Cities Economic Circle was poor. (4) Beijing–Tianjin–Hebei showed mediocre performance in all three aspects. Based on the findings, we make suggestions for MLS development in urban agglomerations for the purpose of achieving high-quality development and supporting China’s overall national transportation network.