Logistics and transportation conditions are important prerequisites for regional development. To clarify the relationship between the level of logistics and transportation in Chongqing’s county areas and the development of rural agricultural production, it takes Chongqing’s county areas as the research region and constructs an evaluation index system centered around the two major systems of county logistics and transportation and agricultural development. The entropy weight method and coupling coordination model are used to analyze the coupling coordination degree between logistics and transportation in Chongqing’s county areas and agricultural production development, and the obstacle degree model is adopted to identify the main factors restricting their coordinated development. The results show that from 2005 to 2020, the coupling coordination degree between logistics and transportation in Chongqing’s county areas and agricultural development showed an upward trend, with the spatial distribution pattern being highest in the main urban area, followed by the western region, then the northeastern region, and finally the southeastern region. The total volume of postal services, fixed assets investment in the logistics and transportation industry, and the total number of trucks are the main obstacles restricting the improvement of the coupling coordination degree between logistics and transportation and agricultural production development. In the future, efforts should be made to leverage the economic radiation of the main urban area, improve transportation infrastructure, develop characteristic mountainous agriculture, and optimize agricultural development models to enhance the coordinated development of logistics and transportation and agricultural production in Chongqing’s county areas.