Rural logistics is particularly important for the sustainable development of Chinese urban agglomeration, which features the coexistence of urban circles and vast countryside. However, the existing literature generally focuses on urban logistics while ignoring rural logistics. Taking the Chengdu-Chongqing agglomeration as an example, this study constructed a rural logistics index system and proposed a new dynamic assessment model for rural logistics development using a fuzzy neural network, Moran index, and Kernel density estimation. The results are as follows: the development of rural logistics has been enhanced, and gaps among cities have gradually narrowed over the past decade. In particular, the spatial distribution of rural logistics showcases a dual-core structure in the Chengdu-Chongqing agglomeration, which is different from the unipolar structure manifested in other urban agglomerations. Because of administrative barriers, the impact from the dual-core cities is very different: Chengdu has a significant spillover effect on its surrounding cities, which is not the case for Chongqing. The findings are of great significance for local governments to provide decision-making support for the sustainable development of urban agglomerations.