Using 125 prefecture-level-and-above cities from China’s ten major unban agglomerations from 2012 to 2023 as samples, this study measures the modernization level of the logistics industrial chain, and analyzes its spatiotemporal characteristics, regional disparities, and evolutionary trends. The findings reveal three key trends. First, the overall modernization level of the logistics industrial chain in the ten major urban agglomerations needs improvement, with significant imbalances observed among cities within each agglomeration. Second, spatial disparities exist in the modernization level, showing a widening trend, with hypervariable density difference identified as the primary source of these spatial disparities. Third, there is a two- or multi-tiered polarization in the modernization level, and the polarization phenomenon is intensifying. Accordingly, it is recommended to strengthen the endogenous drivers for modernizing the logistics industrial chain in each urban agglomeration and explore new avenues for its development, to establish a reasonable urban system to promote coordinated regional development, and to fully consider the heterogeneity among urban agglomerations by formulating tailored policies for the modernization of the logistics industrial chain according to local conditions.