This study introduces the application status of big data and deep learning in the agricultural product logistics supply chain and discusses their impact on the development of agricultural economy. In terms of the coupling and coordination analysis of agricultural product logistics supply chain and agricultural economic development, this article takes Chengdu as an example, constructs a coupling index system and a coupling and coordination degree model of Chengdu logistics supply chain and agricultural economy, and calculates and analyzes them. In terms of analyzing the influencing factors of the integrated development of Chengdu's agricultural product logistics supply chain and agricultural economy, the influencing factors are measured and analyzed from multiple perspectives. According to the results, the foundation of Chengdu's agricultural product logistics supply chain is relatively weak compared to the agricultural economy, and the development of the logistics supply chain cannot keep pace with the development of the agricultural economy. It is unable to fully utilize the advantages of agriculture to drive the development of the agricultural product logistics supply chain. At the same time, the integration potential of Chengdu's culture and agricultural product logistics supply chain is enormous. To effectively promote the high -quality development of agricultural product logistics supply chain, it is necessary to start from five aspects: policy, innovation, technology, talent, and business model. Finally, it is necessary to focus on promoting the transformation of modern science and technology in the logistics supply chain of agricultural products and promote the development of the logistics supply chain of agricultural products with scientific and technological progress, so as to promote the development of agricultural economy. This article aims to explore the role of agricultural product logistics supply chain in the development of agricultural economy in the context of big data and in-depth learning.